Starting phenix.real_space_refine on Fri Jun 13 01:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jb7_6404/06_2025/3jb7_6404.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jb7_6404/06_2025/3jb7_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/cci-nas-00/data/ceres_data/3jb7_6404/06_2025/3jb7_6404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jb7_6404/06_2025/3jb7_6404.map" model { file = "/net/cci-nas-00/data/ceres_data/3jb7_6404/06_2025/3jb7_6404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jb7_6404/06_2025/3jb7_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-5710/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: 8.42, per 1000 atoms: 0.59 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.06 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: 1.82 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: 4.92 Time building geometry restraints manager: 4.68 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: 2 1.61 - 2.44: 42 2.44 - 3.26: 15142 3.26 - 4.08: 34042 4.08 - 4.90: 62597 Warning: very small nonbonded interaction distances. Nonbonded interactions: 111825 Sorted by model distance: nonbonded pdb=" OD1 ASP A1053 " pdb=" NH1 ARG D 117 " model vdw 0.793 3.120 nonbonded pdb=" OD1 ASP A1053 " pdb=" CZ ARG D 117 " model vdw 1.553 3.270 nonbonded pdb=" NH1 ARG B 518 " pdb=" NE2 GLN C 115 " model vdw 1.917 3.200 nonbonded pdb=" OH TYR B 264 " pdb=" O SER C 116 " model vdw 1.936 3.040 nonbonded pdb=" CD ARG A1193 " pdb=" OG SER D 116 " model vdw 1.970 3.440 ... (remaining 111820 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- 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 14502 Z= 0.476 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 Details of bonding type rmsd hydrogen bonds : bond 0.30469 ( 490) hydrogen bonds : angle 9.57494 ( 1389) covalent geometry : bond 0.00709 (14500) covalent geometry : angle 0.76077 (19706) Misc. bond : bond 0.09813 ( 2) *********************** 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 to be fit. rotamer outliers: 17 poor density : 456 time to evaluate : 1.822 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: 0.3209 time to fit residues: 209.0887 Evaluate side-chains 268 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 259 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 B 231 ASN B 436 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.080811 restraints weight = 33961.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083500 restraints weight = 18520.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085413 restraints weight = 12339.307| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14502 Z= 0.218 Angle : 0.681 10.346 19706 Z= 0.354 Chirality : 0.043 0.166 2209 Planarity : 0.004 0.034 2461 Dihedral : 10.646 88.103 2156 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.52 % Allowed : 11.68 % 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: -0.99 (0.19), residues: 1719 helix: -1.22 (0.16), residues: 754 sheet: -1.56 (0.37), residues: 151 loop : 0.37 (0.22), residues: 814 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 0.005 0.001 ARG B 443 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 490) hydrogen bonds : angle 5.72193 ( 1389) covalent geometry : bond 0.00486 (14500) covalent geometry : angle 0.68054 (19706) Misc. bond : bond 0.00462 ( 2) *********************** 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 333 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8192 (t0) cc_final: 0.7964 (m-30) REVERT: A 179 ASP cc_start: 0.7603 (t70) cc_final: 0.7230 (t0) REVERT: A 218 MET cc_start: 0.9329 (mmm) cc_final: 0.8864 (tpp) REVERT: A 237 CYS cc_start: 0.9459 (OUTLIER) cc_final: 0.9032 (t) REVERT: A 240 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 259 GLU cc_start: 0.8563 (tt0) cc_final: 0.8235 (tt0) REVERT: A 350 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8750 (mp0) REVERT: A 354 ASP cc_start: 0.8442 (t0) cc_final: 0.8169 (t0) REVERT: A 361 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8686 (mp) REVERT: A 539 ARG cc_start: 0.4012 (ptt90) cc_final: 0.3417 (ptt-90) REVERT: A 542 LEU cc_start: 0.9411 (tp) cc_final: 0.9165 (tt) REVERT: A 609 CYS cc_start: 0.9159 (m) cc_final: 0.8879 (m) REVERT: A 731 THR cc_start: 0.9262 (m) cc_final: 0.8984 (p) REVERT: A 759 GLU cc_start: 0.8718 (tm-30) cc_final: 0.7312 (tm-30) REVERT: A 779 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8782 (tpp) REVERT: A 788 CYS cc_start: 0.9020 (m) cc_final: 0.8761 (m) REVERT: A 799 LYS cc_start: 0.9123 (mmtp) cc_final: 0.8813 (tptt) REVERT: A 877 ASP cc_start: 0.8908 (t0) cc_final: 0.8267 (t0) REVERT: A 918 ASP cc_start: 0.8675 (m-30) cc_final: 0.8437 (m-30) REVERT: A 939 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8760 (tp40) REVERT: A 1009 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8775 (mmmm) REVERT: A 1072 ARG cc_start: 0.6429 (ttp80) cc_final: 0.5916 (tpt90) REVERT: A 1125 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8510 (ttp-110) REVERT: B 81 ASN cc_start: 0.8808 (p0) cc_final: 0.8165 (t0) REVERT: B 183 ILE cc_start: 0.9095 (mt) cc_final: 0.8860 (pt) REVERT: B 289 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 322 MET cc_start: 0.7589 (mtm) cc_final: 0.4844 (mtp) REVERT: B 522 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.7693 (ttm110) REVERT: B 532 ASP cc_start: 0.8866 (m-30) cc_final: 0.8255 (m-30) REVERT: B 549 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8042 (mm-30) REVERT: C 122 ASN cc_start: 0.9007 (m-40) cc_final: 0.8725 (m-40) REVERT: C 128 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: D 121 PHE cc_start: 0.7446 (t80) cc_final: 0.6762 (t80) outliers start: 53 outliers final: 25 residues processed: 317 average time/residue: 0.2963 time to fit residues: 133.8187 Evaluate side-chains 259 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 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 196 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain D residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 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 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.083847 restraints weight = 34134.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086617 restraints weight = 18442.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088554 restraints weight = 12080.104| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14502 Z= 0.130 Angle : 0.586 8.694 19706 Z= 0.300 Chirality : 0.040 0.149 2209 Planarity : 0.003 0.038 2461 Dihedral : 10.129 87.389 2145 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.32 % Allowed : 14.20 % Favored : 82.48 % 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: -0.43 (0.20), residues: 1719 helix: -0.38 (0.18), residues: 764 sheet: -1.04 (0.36), residues: 157 loop : 0.22 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 445 HIS 0.007 0.001 HIS A 999 PHE 0.010 0.001 PHE C 121 TYR 0.011 0.001 TYR B 178 ARG 0.006 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 490) hydrogen bonds : angle 4.99987 ( 1389) covalent geometry : bond 0.00282 (14500) covalent geometry : angle 0.58623 (19706) Misc. bond : bond 0.00200 ( 2) *********************** 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 301 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 1.674 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 91 ASP cc_start: 0.8119 (t0) cc_final: 0.7866 (m-30) REVERT: A 156 LEU cc_start: 0.9458 (mt) cc_final: 0.9055 (tt) REVERT: A 237 CYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9006 (t) REVERT: A 354 ASP cc_start: 0.8482 (t0) cc_final: 0.8174 (t0) REVERT: A 539 ARG cc_start: 0.3955 (ptt90) cc_final: 0.3265 (ptt-90) REVERT: A 542 LEU cc_start: 0.9272 (tp) cc_final: 0.9033 (tt) REVERT: A 631 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8790 (mtmt) REVERT: A 653 GLN cc_start: 0.8929 (tt0) cc_final: 0.8615 (tt0) REVERT: A 731 THR cc_start: 0.9262 (m) cc_final: 0.8979 (p) REVERT: A 759 GLU cc_start: 0.8668 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 779 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8735 (tpp) REVERT: A 828 MET cc_start: 0.6247 (ppp) cc_final: 0.5954 (ppp) REVERT: A 877 ASP cc_start: 0.8890 (t0) cc_final: 0.8292 (t0) REVERT: A 918 ASP cc_start: 0.8762 (m-30) cc_final: 0.8428 (m-30) REVERT: A 922 LYS cc_start: 0.7900 (tppt) cc_final: 0.7576 (mmmt) REVERT: A 938 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 939 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8702 (tp40) REVERT: A 1072 ARG cc_start: 0.6422 (ttp80) cc_final: 0.5859 (tpt90) REVERT: A 1092 PHE cc_start: 0.7621 (t80) cc_final: 0.7395 (t80) REVERT: B 73 TYR cc_start: 0.8972 (m-80) cc_final: 0.8709 (m-80) REVERT: B 81 ASN cc_start: 0.8779 (p0) cc_final: 0.8121 (t0) REVERT: B 165 GLN cc_start: 0.9301 (mt0) cc_final: 0.8867 (mp10) REVERT: B 183 ILE cc_start: 0.9047 (mt) cc_final: 0.8814 (pt) REVERT: B 449 MET cc_start: 0.8890 (mtp) cc_final: 0.8684 (mmm) REVERT: B 488 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 522 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7742 (ttm110) REVERT: C 119 ASP cc_start: 0.8680 (m-30) cc_final: 0.8420 (m-30) REVERT: C 124 GLN cc_start: 0.8700 (mt0) cc_final: 0.8270 (mt0) REVERT: C 125 PHE cc_start: 0.9103 (t80) cc_final: 0.8886 (t80) REVERT: C 128 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7908 (tm-30) outliers start: 50 outliers final: 23 residues processed: 281 average time/residue: 0.2816 time to fit residues: 114.3165 Evaluate side-chains 237 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 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 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 510 ILE Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 755 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 1078 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 133 VAL 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 465 THR 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 19 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN C 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080633 restraints weight = 34742.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.083280 restraints weight = 18858.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.085115 restraints weight = 12397.325| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14502 Z= 0.230 Angle : 0.647 8.421 19706 Z= 0.330 Chirality : 0.043 0.160 2209 Planarity : 0.004 0.043 2461 Dihedral : 10.092 87.609 2145 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 4.05 % Allowed : 14.93 % Favored : 81.02 % 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: -0.29 (0.20), residues: 1719 helix: -0.07 (0.18), residues: 763 sheet: -0.77 (0.37), residues: 158 loop : 0.02 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.009 0.001 HIS A 28 PHE 0.017 0.002 PHE D 121 TYR 0.022 0.002 TYR A 805 ARG 0.006 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 490) hydrogen bonds : angle 5.12471 ( 1389) covalent geometry : bond 0.00510 (14500) covalent geometry : angle 0.64720 (19706) Misc. bond : bond 0.00408 ( 2) *********************** 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 271 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9410 (mt) cc_final: 0.9115 (tp) REVERT: A 240 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7913 (p0) REVERT: A 266 GLN cc_start: 0.8419 (pp30) cc_final: 0.8151 (pp30) REVERT: A 354 ASP cc_start: 0.8604 (t0) cc_final: 0.8322 (t0) REVERT: A 539 ARG cc_start: 0.3376 (ptt90) cc_final: 0.2946 (ptt90) REVERT: A 542 LEU cc_start: 0.9368 (tp) cc_final: 0.9094 (tt) REVERT: A 683 MET cc_start: 0.8394 (ttt) cc_final: 0.8154 (tmm) REVERT: A 731 THR cc_start: 0.9290 (m) cc_final: 0.9030 (p) REVERT: A 779 MET cc_start: 0.9116 (tpp) cc_final: 0.8643 (tpp) REVERT: A 828 MET cc_start: 0.6294 (ppp) cc_final: 0.5898 (ppp) REVERT: A 877 ASP cc_start: 0.9052 (t0) cc_final: 0.8511 (t0) REVERT: A 918 ASP cc_start: 0.8768 (m-30) cc_final: 0.8424 (m-30) REVERT: A 922 LYS cc_start: 0.7896 (tppt) cc_final: 0.7650 (mmmt) REVERT: A 939 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8822 (tp40) REVERT: A 1072 ARG cc_start: 0.6410 (ttp80) cc_final: 0.5852 (tpt90) REVERT: A 1092 PHE cc_start: 0.7716 (t80) cc_final: 0.7476 (t80) REVERT: A 1143 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9182 (p) REVERT: B 81 ASN cc_start: 0.8805 (p0) cc_final: 0.8228 (t0) REVERT: B 199 ARG cc_start: 0.5559 (ttt-90) cc_final: 0.5133 (ptt-90) REVERT: B 488 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 522 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.7850 (ttm110) REVERT: B 552 GLU cc_start: 0.8685 (tp30) cc_final: 0.8352 (tp30) REVERT: C 124 GLN cc_start: 0.8757 (mt0) cc_final: 0.8417 (mt0) REVERT: C 128 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8036 (tm-30) outliers start: 61 outliers final: 38 residues processed: 252 average time/residue: 0.3699 time to fit residues: 137.1830 Evaluate side-chains 233 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 163 THR 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 259 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 556 THR 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 777 LEU 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 1104 THR Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 267 VAL 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 498 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 133 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 515 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083263 restraints weight = 34786.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.086005 restraints weight = 19131.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087857 restraints weight = 12720.507| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14502 Z= 0.133 Angle : 0.585 12.066 19706 Z= 0.295 Chirality : 0.041 0.200 2209 Planarity : 0.003 0.044 2461 Dihedral : 9.889 86.608 2145 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 2.92 % Allowed : 17.72 % Favored : 79.36 % 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: 0.38 (0.19), residues: 762 sheet: -0.52 (0.37), residues: 158 loop : -0.01 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.011 0.001 HIS A 28 PHE 0.021 0.001 PHE C 121 TYR 0.012 0.001 TYR A1182 ARG 0.009 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 490) hydrogen bonds : angle 4.72846 ( 1389) covalent geometry : bond 0.00300 (14500) covalent geometry : angle 0.58540 (19706) Misc. bond : bond 0.00321 ( 2) *********************** 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 268 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9407 (mt) cc_final: 0.8914 (tt) REVERT: A 237 CYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8968 (t) REVERT: A 266 GLN cc_start: 0.8330 (pp30) cc_final: 0.8039 (pp30) REVERT: A 354 ASP cc_start: 0.8450 (t0) cc_final: 0.8196 (t0) REVERT: A 468 LYS cc_start: 0.9389 (tppt) cc_final: 0.9128 (tptp) REVERT: A 539 ARG cc_start: 0.3559 (ptt90) cc_final: 0.3135 (ptt90) REVERT: A 542 LEU cc_start: 0.9348 (tp) cc_final: 0.9106 (tt) REVERT: A 551 MET cc_start: 0.8584 (mmm) cc_final: 0.7854 (mmm) REVERT: A 563 TYR cc_start: 0.9108 (t80) cc_final: 0.8850 (t80) REVERT: A 631 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8652 (mtpt) REVERT: A 731 THR cc_start: 0.9327 (m) cc_final: 0.9038 (p) REVERT: A 758 MET cc_start: 0.8555 (tmm) cc_final: 0.8242 (ppp) REVERT: A 779 MET cc_start: 0.9092 (tpp) cc_final: 0.8576 (tpp) REVERT: A 828 MET cc_start: 0.6210 (ppp) cc_final: 0.5734 (ppp) REVERT: A 844 GLU cc_start: 0.8155 (mp0) cc_final: 0.7950 (mp0) REVERT: A 877 ASP cc_start: 0.8970 (t0) cc_final: 0.8445 (t0) REVERT: A 918 ASP cc_start: 0.8766 (m-30) cc_final: 0.8498 (m-30) REVERT: A 938 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: A 939 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8798 (tp40) REVERT: A 1056 PHE cc_start: 0.9569 (t80) cc_final: 0.9280 (t80) REVERT: A 1125 ARG cc_start: 0.8706 (ttp-110) cc_final: 0.7978 (ptp90) REVERT: A 1182 TYR cc_start: 0.9097 (t80) cc_final: 0.8887 (t80) REVERT: B 56 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9203 (mm) REVERT: B 81 ASN cc_start: 0.8785 (p0) cc_final: 0.8180 (t0) REVERT: B 165 GLN cc_start: 0.9268 (mt0) cc_final: 0.8857 (mp10) REVERT: B 201 TYR cc_start: 0.8692 (m-10) cc_final: 0.8465 (m-10) REVERT: B 488 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 522 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.7825 (ttm110) REVERT: C 124 GLN cc_start: 0.8749 (mt0) cc_final: 0.8292 (mt0) REVERT: C 128 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7960 (tm-30) outliers start: 44 outliers final: 27 residues processed: 250 average time/residue: 0.4257 time to fit residues: 157.6831 Evaluate side-chains 233 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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 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 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 277 GLU 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 631 LYS Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1044 LEU 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 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR 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 498 ILE 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 83 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN B 182 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082270 restraints weight = 34708.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084922 restraints weight = 18728.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086810 restraints weight = 12387.634| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14502 Z= 0.153 Angle : 0.588 9.657 19706 Z= 0.297 Chirality : 0.041 0.159 2209 Planarity : 0.004 0.048 2461 Dihedral : 9.822 86.741 2145 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 3.58 % Allowed : 17.52 % Favored : 78.90 % 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: 0.09 (0.20), residues: 1719 helix: 0.50 (0.19), residues: 775 sheet: -0.62 (0.36), residues: 174 loop : -0.06 (0.22), residues: 770 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 0.021 0.001 PHE C 121 TYR 0.025 0.001 TYR A 805 ARG 0.010 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 490) hydrogen bonds : angle 4.66012 ( 1389) covalent geometry : bond 0.00341 (14500) covalent geometry : angle 0.58832 (19706) Misc. bond : bond 0.00333 ( 2) *********************** 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 270 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9456 (mt) cc_final: 0.9055 (tt) REVERT: A 237 CYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8980 (t) REVERT: A 354 ASP cc_start: 0.8442 (t0) cc_final: 0.8204 (t0) REVERT: A 539 ARG cc_start: 0.3791 (ptt90) cc_final: 0.3206 (ptt90) REVERT: A 542 LEU cc_start: 0.9348 (tp) cc_final: 0.9111 (tt) REVERT: A 551 MET cc_start: 0.8682 (mmm) cc_final: 0.7937 (tmm) REVERT: A 563 TYR cc_start: 0.9115 (t80) cc_final: 0.8837 (t80) REVERT: A 731 THR cc_start: 0.9326 (m) cc_final: 0.9064 (p) REVERT: A 758 MET cc_start: 0.8479 (tmm) cc_final: 0.7897 (tmm) REVERT: A 779 MET cc_start: 0.9115 (tpp) cc_final: 0.8691 (tpp) REVERT: A 828 MET cc_start: 0.6339 (ppp) cc_final: 0.5685 (ppp) REVERT: A 844 GLU cc_start: 0.8187 (mp0) cc_final: 0.7950 (mp0) REVERT: A 877 ASP cc_start: 0.8990 (t0) cc_final: 0.8458 (t0) REVERT: A 922 LYS cc_start: 0.7896 (tppt) cc_final: 0.7499 (mmmt) REVERT: A 1048 MET cc_start: 0.8835 (tpp) cc_final: 0.8409 (tpp) REVERT: A 1056 PHE cc_start: 0.9537 (t80) cc_final: 0.9278 (t80) REVERT: A 1072 ARG cc_start: 0.6506 (ttp80) cc_final: 0.5956 (tpt90) REVERT: A 1125 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.8021 (ptp90) REVERT: A 1143 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9233 (p) REVERT: A 1182 TYR cc_start: 0.9160 (t80) cc_final: 0.8915 (t80) REVERT: B 56 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9208 (mm) REVERT: B 81 ASN cc_start: 0.8809 (p0) cc_final: 0.8258 (t0) REVERT: B 165 GLN cc_start: 0.9270 (mt0) cc_final: 0.8768 (mp10) REVERT: B 488 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7785 (mt-10) REVERT: B 522 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.7907 (ttm110) REVERT: C 124 GLN cc_start: 0.7984 (mt0) cc_final: 0.7730 (mt0) REVERT: C 128 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7955 (tm-30) outliers start: 54 outliers final: 34 residues processed: 249 average time/residue: 0.3069 time to fit residues: 114.0639 Evaluate side-chains 238 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 163 THR 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 366 VAL Chi-restraints excluded: chain A residue 381 LEU 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 589 VAL Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 777 LEU 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 1143 SER Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 267 VAL 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 498 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 96 optimal weight: 0.0670 chunk 133 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** 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 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.084506 restraints weight = 34148.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087208 restraints weight = 18444.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089152 restraints weight = 12179.985| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14502 Z= 0.106 Angle : 0.585 10.630 19706 Z= 0.292 Chirality : 0.039 0.176 2209 Planarity : 0.003 0.048 2461 Dihedral : 9.641 85.810 2145 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 3.12 % Allowed : 18.38 % 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: 0.20 (0.20), residues: 1719 helix: 0.65 (0.19), residues: 777 sheet: -0.52 (0.39), residues: 162 loop : -0.10 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 445 HIS 0.011 0.001 HIS A 28 PHE 0.015 0.001 PHE C 125 TYR 0.010 0.001 TYR A1182 ARG 0.012 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 490) hydrogen bonds : angle 4.43851 ( 1389) covalent geometry : bond 0.00234 (14500) covalent geometry : angle 0.58521 (19706) Misc. bond : bond 0.00346 ( 2) *********************** 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 277 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9510 (mt) cc_final: 0.9246 (tt) REVERT: A 237 CYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8948 (t) REVERT: A 354 ASP cc_start: 0.8458 (t0) cc_final: 0.8253 (t0) REVERT: A 539 ARG cc_start: 0.3462 (ptt90) cc_final: 0.2841 (ptt90) REVERT: A 542 LEU cc_start: 0.9298 (tp) cc_final: 0.9098 (tt) REVERT: A 551 MET cc_start: 0.8574 (mmm) cc_final: 0.7709 (tmm) REVERT: A 563 TYR cc_start: 0.9126 (t80) cc_final: 0.8837 (t80) REVERT: A 591 GLU cc_start: 0.8189 (tp30) cc_final: 0.7879 (tp30) REVERT: A 683 MET cc_start: 0.8653 (ttp) cc_final: 0.8345 (tmm) REVERT: A 731 THR cc_start: 0.9272 (m) cc_final: 0.9004 (p) REVERT: A 758 MET cc_start: 0.8382 (tmm) cc_final: 0.7878 (tmm) REVERT: A 779 MET cc_start: 0.9119 (tpp) cc_final: 0.8667 (tpp) REVERT: A 828 MET cc_start: 0.6067 (ppp) cc_final: 0.5531 (ppp) REVERT: A 844 GLU cc_start: 0.8210 (mp0) cc_final: 0.7971 (mp0) REVERT: A 877 ASP cc_start: 0.8955 (t0) cc_final: 0.8451 (t0) REVERT: A 890 MET cc_start: 0.8919 (mmm) cc_final: 0.8641 (mmm) REVERT: A 922 LYS cc_start: 0.7964 (tppt) cc_final: 0.7745 (mmmt) REVERT: A 1048 MET cc_start: 0.8954 (tpp) cc_final: 0.8576 (tpp) REVERT: A 1056 PHE cc_start: 0.9532 (t80) cc_final: 0.9281 (t80) REVERT: A 1125 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8006 (ptp90) REVERT: A 1182 TYR cc_start: 0.9073 (t80) cc_final: 0.8869 (t80) REVERT: B 56 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9175 (mm) REVERT: B 81 ASN cc_start: 0.8957 (p0) cc_final: 0.8282 (t0) REVERT: B 165 GLN cc_start: 0.9310 (mt0) cc_final: 0.8779 (mp10) REVERT: B 201 TYR cc_start: 0.8642 (m-10) cc_final: 0.8171 (m-10) REVERT: B 276 ARG cc_start: 0.8653 (ptt180) cc_final: 0.8346 (ptt90) REVERT: B 488 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 522 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7721 (ttm110) REVERT: C 124 GLN cc_start: 0.7973 (mt0) cc_final: 0.7691 (mt0) REVERT: C 128 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: D 121 PHE cc_start: 0.8268 (t80) cc_final: 0.7728 (t80) outliers start: 47 outliers final: 33 residues processed: 259 average time/residue: 0.3764 time to fit residues: 143.9128 Evaluate side-chains 241 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 THR 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 383 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1060 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 12 LEU 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 212 ASN Chi-restraints excluded: chain B residue 267 VAL 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 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 77 optimal weight: 0.6980 chunk 166 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 153 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 141 optimal weight: 0.0170 chunk 119 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** 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 632 ASN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085011 restraints weight = 33885.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087780 restraints weight = 18353.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089691 restraints weight = 12011.942| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14502 Z= 0.105 Angle : 0.593 10.633 19706 Z= 0.295 Chirality : 0.039 0.153 2209 Planarity : 0.004 0.057 2461 Dihedral : 9.552 85.241 2145 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 2.59 % Allowed : 19.91 % Favored : 77.50 % 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: 0.31 (0.20), residues: 1719 helix: 0.68 (0.19), residues: 781 sheet: -0.31 (0.40), residues: 160 loop : -0.01 (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 0.013 0.001 PHE C 125 TYR 0.010 0.001 TYR A1182 ARG 0.013 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 490) hydrogen bonds : angle 4.38252 ( 1389) covalent geometry : bond 0.00232 (14500) covalent geometry : angle 0.59323 (19706) Misc. bond : bond 0.00395 ( 2) *********************** 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 262 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9493 (mt) cc_final: 0.9212 (tt) REVERT: A 237 CYS cc_start: 0.9293 (m) cc_final: 0.8953 (t) REVERT: A 502 MET cc_start: 0.8941 (tpp) cc_final: 0.8048 (tmm) REVERT: A 539 ARG cc_start: 0.3334 (ptt90) cc_final: 0.2681 (ptt90) REVERT: A 551 MET cc_start: 0.8637 (mmm) cc_final: 0.7774 (tmm) REVERT: A 563 TYR cc_start: 0.9097 (t80) cc_final: 0.8800 (t80) REVERT: A 591 GLU cc_start: 0.8180 (tp30) cc_final: 0.7857 (tp30) REVERT: A 731 THR cc_start: 0.9246 (m) cc_final: 0.8958 (p) REVERT: A 758 MET cc_start: 0.8317 (tmm) cc_final: 0.7920 (tmm) REVERT: A 779 MET cc_start: 0.9125 (tpp) cc_final: 0.8653 (tpp) REVERT: A 828 MET cc_start: 0.5913 (ppp) cc_final: 0.5291 (ppp) REVERT: A 844 GLU cc_start: 0.8205 (mp0) cc_final: 0.7930 (mp0) REVERT: A 845 TYR cc_start: 0.8906 (t80) cc_final: 0.8614 (t80) REVERT: A 877 ASP cc_start: 0.8929 (t0) cc_final: 0.8431 (t0) REVERT: A 890 MET cc_start: 0.9015 (mmm) cc_final: 0.8792 (mmm) REVERT: A 918 ASP cc_start: 0.8544 (m-30) cc_final: 0.8186 (m-30) REVERT: A 1041 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8536 (p90) REVERT: A 1048 MET cc_start: 0.8937 (tpp) cc_final: 0.8133 (mmm) REVERT: A 1056 PHE cc_start: 0.9510 (t80) cc_final: 0.9252 (t80) REVERT: A 1072 ARG cc_start: 0.6318 (ttp80) cc_final: 0.5859 (tpt90) REVERT: A 1182 TYR cc_start: 0.9089 (t80) cc_final: 0.8849 (t80) REVERT: B 56 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9172 (mm) REVERT: B 81 ASN cc_start: 0.9216 (p0) cc_final: 0.8314 (t0) REVERT: B 165 GLN cc_start: 0.9296 (mt0) cc_final: 0.8779 (mp10) REVERT: B 201 TYR cc_start: 0.8659 (m-10) cc_final: 0.8314 (m-10) REVERT: B 276 ARG cc_start: 0.8571 (ptt180) cc_final: 0.8264 (ptt90) REVERT: B 436 GLN cc_start: 0.8563 (mt0) cc_final: 0.8278 (mt0) REVERT: B 488 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 522 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.7701 (ttm110) REVERT: C 124 GLN cc_start: 0.7929 (mt0) cc_final: 0.7618 (mt0) REVERT: C 128 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: D 121 PHE cc_start: 0.8252 (t80) cc_final: 0.7730 (t80) outliers start: 39 outliers final: 30 residues processed: 247 average time/residue: 0.3962 time to fit residues: 141.8071 Evaluate side-chains 236 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 418 LEU 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 1060 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 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU 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 140 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.084175 restraints weight = 34336.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086875 restraints weight = 18643.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088683 restraints weight = 12216.571| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14502 Z= 0.139 Angle : 0.613 10.720 19706 Z= 0.306 Chirality : 0.040 0.147 2209 Planarity : 0.004 0.065 2461 Dihedral : 9.567 85.030 2145 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 2.92 % Allowed : 19.84 % Favored : 77.24 % 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: 0.75 (0.19), residues: 781 sheet: -0.23 (0.38), residues: 172 loop : -0.03 (0.22), residues: 766 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 0.017 0.001 PHE A 142 TYR 0.012 0.001 TYR B 264 ARG 0.013 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 490) hydrogen bonds : angle 4.44737 ( 1389) covalent geometry : bond 0.00315 (14500) covalent geometry : angle 0.61305 (19706) Misc. bond : bond 0.00466 ( 2) *********************** 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 247 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9505 (mt) cc_final: 0.9232 (tt) REVERT: A 237 CYS cc_start: 0.9341 (m) cc_final: 0.9004 (t) REVERT: A 539 ARG cc_start: 0.3063 (ptt90) cc_final: 0.2485 (ptt90) REVERT: A 551 MET cc_start: 0.8684 (mmm) cc_final: 0.7756 (tmm) REVERT: A 591 GLU cc_start: 0.8228 (tp30) cc_final: 0.7919 (tp30) REVERT: A 683 MET cc_start: 0.8482 (ttp) cc_final: 0.8051 (tmm) REVERT: A 731 THR cc_start: 0.9271 (m) cc_final: 0.9001 (p) REVERT: A 758 MET cc_start: 0.8292 (tmm) cc_final: 0.7910 (tmm) REVERT: A 779 MET cc_start: 0.9082 (tpp) cc_final: 0.8606 (tpp) REVERT: A 828 MET cc_start: 0.6010 (ppp) cc_final: 0.5215 (ppp) REVERT: A 844 GLU cc_start: 0.8211 (mp0) cc_final: 0.7933 (mp0) REVERT: A 877 ASP cc_start: 0.8953 (t0) cc_final: 0.8460 (t0) REVERT: A 1041 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8541 (p90) REVERT: A 1048 MET cc_start: 0.8938 (tpp) cc_final: 0.8147 (mmm) REVERT: A 1056 PHE cc_start: 0.9536 (t80) cc_final: 0.9245 (t80) REVERT: A 1072 ARG cc_start: 0.6406 (ttp80) cc_final: 0.5948 (tpt90) REVERT: B 56 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9176 (mm) REVERT: B 81 ASN cc_start: 0.8979 (p0) cc_final: 0.8258 (t0) REVERT: B 165 GLN cc_start: 0.9310 (mt0) cc_final: 0.8799 (mp10) REVERT: B 201 TYR cc_start: 0.8551 (m-10) cc_final: 0.8267 (m-10) REVERT: B 276 ARG cc_start: 0.8585 (ptt180) cc_final: 0.8287 (ptt90) REVERT: B 436 GLN cc_start: 0.8569 (mt0) cc_final: 0.8223 (mt0) REVERT: B 488 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7802 (mt-10) REVERT: B 522 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7719 (ttm110) REVERT: C 124 GLN cc_start: 0.7975 (mt0) cc_final: 0.7772 (mp10) REVERT: C 128 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: D 121 PHE cc_start: 0.8278 (t80) cc_final: 0.7717 (t80) outliers start: 44 outliers final: 34 residues processed: 234 average time/residue: 0.3489 time to fit residues: 121.2689 Evaluate side-chains 235 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 418 LEU 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 1060 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 12 LEU 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 267 VAL 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 514 THR 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 13 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.085024 restraints weight = 34197.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.087724 restraints weight = 18572.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089593 restraints weight = 12162.176| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14502 Z= 0.124 Angle : 0.627 12.072 19706 Z= 0.310 Chirality : 0.040 0.161 2209 Planarity : 0.004 0.065 2461 Dihedral : 9.537 84.873 2145 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 2.65 % Allowed : 20.70 % Favored : 76.64 % 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: 0.41 (0.20), residues: 1719 helix: 0.77 (0.19), residues: 778 sheet: -0.14 (0.39), residues: 172 loop : 0.00 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 445 HIS 0.012 0.001 HIS A 28 PHE 0.016 0.001 PHE C 125 TYR 0.027 0.001 TYR A1182 ARG 0.014 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 490) hydrogen bonds : angle 4.42769 ( 1389) covalent geometry : bond 0.00283 (14500) covalent geometry : angle 0.62652 (19706) Misc. bond : bond 0.00440 ( 2) ********************** 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 243 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9502 (mt) cc_final: 0.9229 (tt) REVERT: A 237 CYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9004 (t) REVERT: A 502 MET cc_start: 0.8932 (tpp) cc_final: 0.8024 (tmm) REVERT: A 539 ARG cc_start: 0.3248 (ptt90) cc_final: 0.2709 (ptt90) REVERT: A 551 MET cc_start: 0.8666 (mmm) cc_final: 0.7759 (tmm) REVERT: A 591 GLU cc_start: 0.8185 (tp30) cc_final: 0.7853 (tp30) REVERT: A 683 MET cc_start: 0.8559 (ttp) cc_final: 0.8197 (tmm) REVERT: A 731 THR cc_start: 0.9264 (m) cc_final: 0.8984 (p) REVERT: A 758 MET cc_start: 0.8216 (tmm) cc_final: 0.7869 (tmm) REVERT: A 779 MET cc_start: 0.9067 (tpp) cc_final: 0.8595 (tpp) REVERT: A 828 MET cc_start: 0.5929 (ppp) cc_final: 0.5063 (ppp) REVERT: A 844 GLU cc_start: 0.8206 (mp0) cc_final: 0.7938 (mp0) REVERT: A 877 ASP cc_start: 0.8947 (t0) cc_final: 0.8375 (t0) REVERT: A 918 ASP cc_start: 0.8270 (m-30) cc_final: 0.7950 (m-30) REVERT: A 1041 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8534 (p90) REVERT: A 1048 MET cc_start: 0.8941 (tpp) cc_final: 0.8139 (mmm) REVERT: A 1056 PHE cc_start: 0.9525 (t80) cc_final: 0.9245 (t80) REVERT: A 1125 ARG cc_start: 0.8756 (ptp90) cc_final: 0.8304 (ptp90) REVERT: A 1133 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5932 (p90) REVERT: B 56 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9183 (mm) REVERT: B 81 ASN cc_start: 0.8861 (p0) cc_final: 0.8201 (t0) REVERT: B 165 GLN cc_start: 0.9313 (mt0) cc_final: 0.8792 (mp10) REVERT: B 201 TYR cc_start: 0.8532 (m-10) cc_final: 0.8267 (m-10) REVERT: B 276 ARG cc_start: 0.8565 (ptt180) cc_final: 0.8269 (ptt90) REVERT: B 436 GLN cc_start: 0.8534 (mt0) cc_final: 0.8157 (mt0) REVERT: B 447 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9401 (mtmm) REVERT: B 488 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 522 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.7711 (ttm110) REVERT: C 124 GLN cc_start: 0.7968 (mt0) cc_final: 0.7679 (mt0) REVERT: C 128 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: D 121 PHE cc_start: 0.8775 (t80) cc_final: 0.8200 (t80) outliers start: 40 outliers final: 31 residues processed: 229 average time/residue: 0.2737 time to fit residues: 91.5088 Evaluate side-chains 233 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 418 LEU 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 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 1060 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 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 514 THR 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 64 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS A 480 GLN ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.081835 restraints weight = 35251.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.084476 restraints weight = 19188.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.086261 restraints weight = 12631.952| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14502 Z= 0.207 Angle : 0.678 11.852 19706 Z= 0.339 Chirality : 0.042 0.176 2209 Planarity : 0.004 0.073 2461 Dihedral : 9.686 85.475 2145 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 2.72 % Allowed : 20.84 % Favored : 76.44 % 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: 0.22 (0.20), residues: 1719 helix: 0.65 (0.19), residues: 782 sheet: -0.28 (0.39), residues: 172 loop : -0.14 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.012 0.001 HIS A 28 PHE 0.019 0.001 PHE A 142 TYR 0.026 0.001 TYR A1182 ARG 0.014 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 490) hydrogen bonds : angle 4.68119 ( 1389) covalent geometry : bond 0.00464 (14500) covalent geometry : angle 0.67829 (19706) Misc. bond : bond 0.00472 ( 2) =============================================================================== Job complete usr+sys time: 4838.54 seconds wall clock time: 88 minutes 3.88 seconds (5283.88 seconds total)