Starting phenix.real_space_refine on Thu Mar 5 10:18:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sl1_10234/03_2026/6sl1_10234.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sl1_10234/03_2026/6sl1_10234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sl1_10234/03_2026/6sl1_10234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sl1_10234/03_2026/6sl1_10234.map" model { file = "/net/cci-nas-00/data/ceres_data/6sl1_10234/03_2026/6sl1_10234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sl1_10234/03_2026/6sl1_10234.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 13371 2.51 5 N 3670 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2652, 21009 Classifications: {'peptide': 2652} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 112, 'TRANS': 2538} Chain breaks: 19 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.48, per 1000 atoms: 0.21 Number of scatterers: 21041 At special positions: 0 Unit cell: (114.372, 140.847, 210.741, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 3 15.00 Mg 1 11.99 O 3900 8.00 N 3670 7.00 C 13371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1447 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 749.8 milliseconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5090 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 5 sheets defined 70.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 removed outlier: 4.033A pdb=" N LEU A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.574A pdb=" N ILE A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 72 removed outlier: 3.629A pdb=" N ARG A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.767A pdb=" N ARG A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.998A pdb=" N ALA A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 4.020A pdb=" N LYS A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 removed outlier: 3.891A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 176 " --> pdb=" O CYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.555A pdb=" N ASP A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.541A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 283 through 299 removed outlier: 3.673A pdb=" N CYS A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 327 through 328 No H-bonds generated for 'chain 'A' and resid 327 through 328' Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.058A pdb=" N TRP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.536A pdb=" N ARG A 361 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 467 Processing helix chain 'A' and resid 467 through 474 removed outlier: 4.242A pdb=" N HIS A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.997A pdb=" N ASP A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 4.572A pdb=" N MET A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.160A pdb=" N TRP A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.759A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.142A pdb=" N ILE A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 598 removed outlier: 4.430A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 621 removed outlier: 4.097A pdb=" N SER A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 616 " --> pdb=" O HIS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 637 through 646 removed outlier: 3.648A pdb=" N VAL A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 removed outlier: 4.213A pdb=" N TRP A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 676 " --> pdb=" O LYS A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 737 removed outlier: 3.930A pdb=" N ARG A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Proline residue: A 730 - end of helix Processing helix chain 'A' and resid 755 through 769 removed outlier: 3.645A pdb=" N ARG A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 761 " --> pdb=" O ARG A 757 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.720A pdb=" N VAL A 776 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.508A pdb=" N GLU A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 801 Processing helix chain 'A' and resid 809 through 819 removed outlier: 3.914A pdb=" N ILE A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 826 through 835 removed outlier: 4.188A pdb=" N ALA A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 removed outlier: 4.071A pdb=" N GLU A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 857 removed outlier: 3.581A pdb=" N ARG A 857 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 removed outlier: 4.331A pdb=" N SER A 897 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 898 " --> pdb=" O LEU A 895 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 894 through 898' Processing helix chain 'A' and resid 899 through 919 removed outlier: 3.711A pdb=" N PHE A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 904 " --> pdb=" O PRO A 900 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 907 " --> pdb=" O PHE A 903 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 917 " --> pdb=" O PHE A 913 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.924A pdb=" N GLU A 923 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 936 removed outlier: 4.037A pdb=" N ILE A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.596A pdb=" N ILE A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 954 " --> pdb=" O MET A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 954' Processing helix chain 'A' and resid 961 through 977 removed outlier: 3.892A pdb=" N ALA A 965 " --> pdb=" O PRO A 961 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 removed outlier: 3.732A pdb=" N ASP A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 999 No H-bonds generated for 'chain 'A' and resid 997 through 999' Processing helix chain 'A' and resid 1011 through 1023 removed outlier: 4.220A pdb=" N TYR A1019 " --> pdb=" O ASP A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 3.645A pdb=" N ARG A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1041 " --> pdb=" O ARG A1037 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 3.646A pdb=" N LEU A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1084 removed outlier: 3.647A pdb=" N TYR A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1082 " --> pdb=" O HIS A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 removed outlier: 4.091A pdb=" N PHE A1088 " --> pdb=" O PRO A1085 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1090 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1095 through 1107 removed outlier: 4.385A pdb=" N VAL A1101 " --> pdb=" O ASP A1097 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A1102 " --> pdb=" O ASP A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1129 removed outlier: 4.632A pdb=" N PHE A1119 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A1126 " --> pdb=" O PHE A1122 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1133 No H-bonds generated for 'chain 'A' and resid 1131 through 1133' Processing helix chain 'A' and resid 1134 through 1145 removed outlier: 3.609A pdb=" N ILE A1145 " --> pdb=" O HIS A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1178 removed outlier: 3.664A pdb=" N ALA A1163 " --> pdb=" O VAL A1159 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A1165 " --> pdb=" O HIS A1161 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1166 " --> pdb=" O SER A1162 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A1167 " --> pdb=" O ALA A1163 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 removed outlier: 4.277A pdb=" N LEU A1185 " --> pdb=" O GLY A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.674A pdb=" N LEU A1193 " --> pdb=" O PHE A1189 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A1196 " --> pdb=" O GLN A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1213 removed outlier: 3.627A pdb=" N GLY A1212 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A1213 " --> pdb=" O ILE A1210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1209 through 1213' Processing helix chain 'A' and resid 1215 through 1234 removed outlier: 3.679A pdb=" N LEU A1219 " --> pdb=" O SER A1215 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A1226 " --> pdb=" O GLU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.765A pdb=" N SER A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 removed outlier: 3.732A pdb=" N ASP A1270 " --> pdb=" O SER A1266 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1302 removed outlier: 7.048A pdb=" N LYS A1292 " --> pdb=" O LYS A1288 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N GLU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A1294 " --> pdb=" O LEU A1290 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A1296 " --> pdb=" O LYS A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1313 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 3.895A pdb=" N PHE A1324 " --> pdb=" O ILE A1320 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1344 Processing helix chain 'A' and resid 1362 through 1373 removed outlier: 3.999A pdb=" N VAL A1368 " --> pdb=" O PRO A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1398 removed outlier: 3.808A pdb=" N ILE A1398 " --> pdb=" O LEU A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1402 Processing helix chain 'A' and resid 1403 through 1422 removed outlier: 4.105A pdb=" N ALA A1407 " --> pdb=" O GLY A1403 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A1408 " --> pdb=" O PRO A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1443 removed outlier: 3.749A pdb=" N GLU A1432 " --> pdb=" O GLY A1428 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1440 " --> pdb=" O HIS A1436 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1443 " --> pdb=" O ARG A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1462 Processing helix chain 'A' and resid 1469 through 1490 Processing helix chain 'A' and resid 1498 through 1521 Processing helix chain 'A' and resid 1529 through 1544 removed outlier: 3.609A pdb=" N LYS A1533 " --> pdb=" O ASP A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1570 removed outlier: 4.025A pdb=" N GLY A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1585 removed outlier: 3.740A pdb=" N VAL A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1584 " --> pdb=" O ALA A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1612 removed outlier: 3.915A pdb=" N LYS A1611 " --> pdb=" O GLU A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1620 Processing helix chain 'A' and resid 1626 through 1645 removed outlier: 3.790A pdb=" N LEU A1630 " --> pdb=" O GLY A1626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1642 " --> pdb=" O GLY A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1664 Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.611A pdb=" N GLY A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1688 through 1708 Processing helix chain 'A' and resid 1709 through 1720 Processing helix chain 'A' and resid 1721 through 1727 Processing helix chain 'A' and resid 1761 through 1772 Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.600A pdb=" N VAL A1782 " --> pdb=" O VAL A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1790 removed outlier: 4.487A pdb=" N ILE A1786 " --> pdb=" O VAL A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1809 removed outlier: 3.841A pdb=" N ARG A1796 " --> pdb=" O GLY A1792 " (cutoff:3.500A) Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1814 through 1828 removed outlier: 3.740A pdb=" N ARG A1818 " --> pdb=" O GLN A1814 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 3.805A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1863 Processing helix chain 'A' and resid 1870 through 1881 Processing helix chain 'A' and resid 1883 through 1899 Processing helix chain 'A' and resid 1915 through 1924 removed outlier: 4.168A pdb=" N GLU A1919 " --> pdb=" O ASP A1915 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1933 Processing helix chain 'A' and resid 1938 through 1949 Processing helix chain 'A' and resid 1952 through 1969 removed outlier: 3.790A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1989 removed outlier: 3.781A pdb=" N GLY A1989 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 1999 removed outlier: 3.556A pdb=" N SER A1994 " --> pdb=" O LEU A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2022 Processing helix chain 'A' and resid 2034 through 2048 removed outlier: 3.511A pdb=" N THR A2038 " --> pdb=" O SER A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2051 through 2072 removed outlier: 3.817A pdb=" N VAL A2055 " --> pdb=" O GLU A2051 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A2057 " --> pdb=" O ASP A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2098 removed outlier: 3.644A pdb=" N ASN A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2101 through 2120 removed outlier: 3.535A pdb=" N LEU A2105 " --> pdb=" O ASP A2101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A2117 " --> pdb=" O GLU A2113 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP A2118 " --> pdb=" O LYS A2114 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2144 removed outlier: 3.597A pdb=" N ILE A2130 " --> pdb=" O ASP A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2175 Processing helix chain 'A' and resid 2177 through 2190 Processing helix chain 'A' and resid 2191 through 2198 removed outlier: 3.592A pdb=" N SER A2197 " --> pdb=" O PRO A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2217 Processing helix chain 'A' and resid 2219 through 2233 Processing helix chain 'A' and resid 2244 through 2259 Processing helix chain 'A' and resid 2266 through 2271 Processing helix chain 'A' and resid 2271 through 2279 Processing helix chain 'A' and resid 2285 through 2304 Processing helix chain 'A' and resid 2305 through 2329 Processing helix chain 'A' and resid 2348 through 2386 Processing helix chain 'A' and resid 2393 through 2405 removed outlier: 3.608A pdb=" N LYS A2405 " --> pdb=" O LEU A2401 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2419 removed outlier: 3.517A pdb=" N ASN A2412 " --> pdb=" O GLU A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2420 through 2422 No H-bonds generated for 'chain 'A' and resid 2420 through 2422' Processing helix chain 'A' and resid 2423 through 2429 removed outlier: 3.817A pdb=" N ALA A2428 " --> pdb=" O ARG A2425 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A2429 " --> pdb=" O LYS A2426 " (cutoff:3.500A) Processing helix chain 'A' and resid 2430 through 2435 Processing helix chain 'A' and resid 2443 through 2460 removed outlier: 3.735A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2474 removed outlier: 5.657A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2498 removed outlier: 4.153A pdb=" N ARG A2486 " --> pdb=" O VAL A2482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2506 through 2523 Processing helix chain 'A' and resid 2540 through 2553 Processing helix chain 'A' and resid 2615 through 2633 removed outlier: 4.213A pdb=" N ASP A2619 " --> pdb=" O ASP A2615 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2642 removed outlier: 3.669A pdb=" N ARG A2642 " --> pdb=" O GLU A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2682 Proline residue: A2676 - end of helix removed outlier: 3.966A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2687 through 2698 removed outlier: 3.824A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2702 through 2715 Processing helix chain 'A' and resid 2720 through 2722 No H-bonds generated for 'chain 'A' and resid 2720 through 2722' Processing helix chain 'A' and resid 2723 through 2728 Processing helix chain 'A' and resid 2731 through 2756 removed outlier: 4.024A pdb=" N GLN A2737 " --> pdb=" O ASP A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2785 through 2789 removed outlier: 3.730A pdb=" N VAL A2789 " --> pdb=" O MET A2786 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2807 Processing helix chain 'A' and resid 2815 through 2829 Processing helix chain 'A' and resid 2831 through 2844 Processing helix chain 'A' and resid 2853 through 2861 removed outlier: 3.831A pdb=" N GLN A2861 " --> pdb=" O MET A2857 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2910 removed outlier: 3.513A pdb=" N LEU A2910 " --> pdb=" O VAL A2906 " (cutoff:3.500A) Processing helix chain 'A' and resid 2915 through 2928 removed outlier: 3.529A pdb=" N THR A2928 " --> pdb=" O ILE A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2929 through 2934 Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 1550 through 1551 removed outlier: 7.275A pdb=" N GLY A1550 " --> pdb=" O ASN A1593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 2534 through 2536 removed outlier: 7.158A pdb=" N GLU A2582 " --> pdb=" O THR A2596 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR A2596 " --> pdb=" O GLU A2582 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2534 through 2536 removed outlier: 7.158A pdb=" N GLU A2582 " --> pdb=" O THR A2596 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR A2596 " --> pdb=" O GLU A2582 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER A2658 " --> pdb=" O LEU A2654 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2667 through 2669 1088 hydrogen bonds defined for protein. 3174 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: 4.59 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7281 1.36 - 1.51: 6789 1.51 - 1.65: 7234 1.65 - 1.80: 126 1.80 - 1.95: 24 Bond restraints: 21454 Sorted by residual: bond pdb=" N PRO A1378 " pdb=" CD PRO A1378 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" CG LEU A2084 " pdb=" CD2 LEU A2084 " ideal model delta sigma weight residual 1.521 1.412 0.109 3.30e-02 9.18e+02 1.08e+01 bond pdb=" CG LEU A2608 " pdb=" CD1 LEU A2608 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.03e+01 bond pdb=" CB VAL A2067 " pdb=" CG2 VAL A2067 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CA SER A 897 " pdb=" C SER A 897 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.80e-02 3.09e+03 6.05e+00 ... (remaining 21449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 28588 2.59 - 5.17: 439 5.17 - 7.76: 36 7.76 - 10.35: 5 10.35 - 12.93: 4 Bond angle restraints: 29072 Sorted by residual: angle pdb=" CA PRO A1378 " pdb=" N PRO A1378 " pdb=" CD PRO A1378 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.53e+01 angle pdb=" N VAL A2482 " pdb=" CA VAL A2482 " pdb=" C VAL A2482 " ideal model delta sigma weight residual 109.34 119.20 -9.86 2.08e+00 2.31e-01 2.25e+01 angle pdb=" C VAL A2482 " pdb=" CA VAL A2482 " pdb=" CB VAL A2482 " ideal model delta sigma weight residual 111.29 105.49 5.80 1.64e+00 3.72e-01 1.25e+01 angle pdb=" CA LEU A1652 " pdb=" CB LEU A1652 " pdb=" CG LEU A1652 " ideal model delta sigma weight residual 116.30 127.71 -11.41 3.50e+00 8.16e-02 1.06e+01 angle pdb=" CB LEU A2608 " pdb=" CG LEU A2608 " pdb=" CD1 LEU A2608 " ideal model delta sigma weight residual 110.70 101.66 9.04 3.00e+00 1.11e-01 9.07e+00 ... (remaining 29067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 12608 30.39 - 60.79: 449 60.79 - 91.18: 30 91.18 - 121.57: 0 121.57 - 151.96: 1 Dihedral angle restraints: 13088 sinusoidal: 5289 harmonic: 7799 Sorted by residual: dihedral pdb=" CA GLU A2481 " pdb=" C GLU A2481 " pdb=" N VAL A2482 " pdb=" CA VAL A2482 " ideal model delta harmonic sigma weight residual -180.00 -123.75 -56.25 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA MET A 677 " pdb=" C MET A 677 " pdb=" N GLU A 678 " pdb=" CA GLU A 678 " ideal model delta harmonic sigma weight residual 180.00 146.14 33.86 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA MET A 259 " pdb=" C MET A 259 " pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta harmonic sigma weight residual -180.00 -148.85 -31.15 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 13085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1828 0.037 - 0.074: 1108 0.074 - 0.110: 307 0.110 - 0.147: 84 0.147 - 0.184: 6 Chirality restraints: 3333 Sorted by residual: chirality pdb=" CB ILE A2852 " pdb=" CA ILE A2852 " pdb=" CG1 ILE A2852 " pdb=" CG2 ILE A2852 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CA PRO A2732 " pdb=" N PRO A2732 " pdb=" C PRO A2732 " pdb=" CB PRO A2732 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ARG A1863 " pdb=" N ARG A1863 " pdb=" C ARG A1863 " pdb=" CB ARG A1863 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 3330 not shown) Planarity restraints: 3710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1377 " 0.131 5.00e-02 4.00e+02 1.84e-01 5.42e+01 pdb=" N PRO A1378 " -0.318 5.00e-02 4.00e+02 pdb=" CA PRO A1378 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO A1378 " 0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A2481 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU A2481 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU A2481 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A2482 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1443 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C VAL A1443 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A1443 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A1444 " 0.013 2.00e-02 2.50e+03 ... (remaining 3707 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 253 2.59 - 3.17: 18813 3.17 - 3.75: 30944 3.75 - 4.32: 44766 4.32 - 4.90: 73815 Nonbonded interactions: 168591 Sorted by model distance: nonbonded pdb=" O2A AGS A3001 " pdb="MG MG A3002 " model vdw 2.016 2.170 nonbonded pdb=" NH1 ARG A2647 " pdb=" OE2 GLU A2774 " model vdw 2.064 3.120 nonbonded pdb=" O ASN A 569 " pdb=" OG1 THR A 573 " model vdw 2.065 3.040 nonbonded pdb=" OD1 ASP A2012 " pdb=" OG SER A2034 " model vdw 2.097 3.040 nonbonded pdb=" O ALA A 764 " pdb=" OG1 THR A 767 " model vdw 2.101 3.040 ... (remaining 168586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.011 0.109 21455 Z= 0.449 Angle : 0.826 12.933 29074 Z= 0.436 Chirality : 0.048 0.184 3333 Planarity : 0.006 0.184 3710 Dihedral : 14.944 151.964 7995 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.42 % Rotamer: Outliers : 6.72 % Allowed : 9.17 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.13), residues: 2612 helix: -2.51 (0.10), residues: 1720 sheet: -1.78 (0.85), residues: 31 loop : -3.58 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2799 TYR 0.022 0.002 TYR A2742 PHE 0.023 0.002 PHE A2724 TRP 0.023 0.003 TRP A2940 HIS 0.008 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.01060 (21454) covalent geometry : angle 0.82518 (29072) SS BOND : bond 0.00585 ( 1) SS BOND : angle 3.60055 ( 2) hydrogen bonds : bond 0.22624 ( 1084) hydrogen bonds : angle 8.01403 ( 3174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 455 time to evaluate : 0.839 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: A 136 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.5074 (pt) REVERT: A 269 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 272 PHE cc_start: 0.7664 (t80) cc_final: 0.7406 (t80) REVERT: A 274 ILE cc_start: 0.8125 (mt) cc_final: 0.7920 (mp) REVERT: A 327 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7971 (m) REVERT: A 330 TYR cc_start: 0.8547 (m-80) cc_final: 0.7742 (m-80) REVERT: A 358 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.6105 (t80) REVERT: A 366 ARG cc_start: 0.6604 (mtm180) cc_final: 0.5962 (mtp-110) REVERT: A 450 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7164 (t70) REVERT: A 601 MET cc_start: 0.7339 (mtp) cc_final: 0.6906 (mtt) REVERT: A 671 TRP cc_start: 0.7972 (t60) cc_final: 0.7723 (t60) REVERT: A 892 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6460 (mtt-85) REVERT: A 947 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7416 (ptm160) REVERT: A 980 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: A 1051 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5496 (pp20) REVERT: A 1075 LYS cc_start: 0.7887 (mttt) cc_final: 0.7336 (mptt) REVERT: A 1185 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 1204 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: A 1314 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8330 (p90) REVERT: A 1316 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: A 1558 GLU cc_start: 0.7516 (mp0) cc_final: 0.7300 (mt-10) REVERT: A 1709 ASP cc_start: 0.6866 (m-30) cc_final: 0.6641 (m-30) REVERT: A 1968 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.6364 (tpm170) outliers start: 154 outliers final: 80 residues processed: 586 average time/residue: 0.1673 time to fit residues: 145.7098 Evaluate side-chains 344 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 250 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain A residue 892 ARG Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 997 SER Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1204 GLN Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1258 SER Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1316 GLN Chi-restraints excluded: chain A residue 1372 SER Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2410 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2649 TYR Chi-restraints excluded: chain A residue 2792 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 252 GLN A 293 GLN A 418 HIS A 454 HIS A 607 GLN A 643 ASN A 933 ASN A1027 ASN A1062 GLN A1106 HIS A1192 GLN A1298 ASN A1345 HIS A1354 GLN A1551 ASN A1574 GLN A1577 ASN A1656 GLN A1665 GLN A1676 ASN A1844 ASN A1870 ASN A2175 HIS A2179 GLN A2239 GLN A2255 GLN A2294 GLN A2354 GLN A2356 GLN A2360 GLN A2446 GLN A2518 HIS A2572 HIS A2624 GLN A2641 GLN A2678 HIS A2754 HIS A2861 GLN A2925 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123611 restraints weight = 35573.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122396 restraints weight = 35102.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123975 restraints weight = 36304.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124396 restraints weight = 23179.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124890 restraints weight = 21667.622| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21455 Z= 0.152 Angle : 0.674 10.997 29074 Z= 0.340 Chirality : 0.042 0.323 3333 Planarity : 0.005 0.069 3710 Dihedral : 9.517 157.444 3073 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 4.54 % Allowed : 14.40 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.15), residues: 2612 helix: -0.81 (0.12), residues: 1773 sheet: -0.80 (0.91), residues: 31 loop : -2.72 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 682 TYR 0.014 0.001 TYR A1457 PHE 0.032 0.001 PHE A2112 TRP 0.015 0.002 TRP A1382 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00336 (21454) covalent geometry : angle 0.67361 (29072) SS BOND : bond 0.00020 ( 1) SS BOND : angle 1.15098 ( 2) hydrogen bonds : bond 0.04954 ( 1084) hydrogen bonds : angle 4.64792 ( 3174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 303 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.6092 (m-80) cc_final: 0.5823 (m-80) REVERT: A 109 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6522 (mt) REVERT: A 136 LEU cc_start: 0.5010 (OUTLIER) cc_final: 0.4788 (pt) REVERT: A 248 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5622 (t-90) REVERT: A 269 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 274 ILE cc_start: 0.7762 (mt) cc_final: 0.7454 (mp) REVERT: A 327 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 330 TYR cc_start: 0.8307 (m-80) cc_final: 0.7543 (m-80) REVERT: A 366 ARG cc_start: 0.6489 (mtm180) cc_final: 0.5950 (mtp-110) REVERT: A 450 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6670 (t70) REVERT: A 601 MET cc_start: 0.7265 (mtp) cc_final: 0.6888 (mtt) REVERT: A 641 LEU cc_start: 0.8429 (tt) cc_final: 0.8093 (mp) REVERT: A 811 PHE cc_start: 0.5071 (OUTLIER) cc_final: 0.4677 (t80) REVERT: A 947 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7501 (ptm160) REVERT: A 1051 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5661 (pp20) REVERT: A 1249 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8487 (pp) REVERT: A 1442 VAL cc_start: 0.8452 (t) cc_final: 0.8220 (t) REVERT: A 1871 MET cc_start: 0.8725 (mmt) cc_final: 0.8450 (mmt) REVERT: A 1968 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6557 (tpp-160) REVERT: A 2147 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 2382 LEU cc_start: 0.8517 (mt) cc_final: 0.8274 (mt) REVERT: A 2660 LEU cc_start: 0.8594 (mp) cc_final: 0.8384 (mp) REVERT: A 2836 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 104 outliers final: 47 residues processed: 386 average time/residue: 0.1508 time to fit residues: 90.2758 Evaluate side-chains 283 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 225 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 997 SER Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1266 SER Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 139 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 383 HIS A 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123182 restraints weight = 35611.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121746 restraints weight = 36394.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123197 restraints weight = 36624.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123700 restraints weight = 24192.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124118 restraints weight = 22182.304| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21455 Z= 0.146 Angle : 0.618 10.068 29074 Z= 0.307 Chirality : 0.041 0.406 3333 Planarity : 0.004 0.054 3710 Dihedral : 8.073 157.262 2970 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.88 % Allowed : 16.24 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2612 helix: -0.13 (0.12), residues: 1796 sheet: -0.61 (0.94), residues: 33 loop : -2.51 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1287 TYR 0.015 0.001 TYR A2649 PHE 0.022 0.001 PHE A2112 TRP 0.017 0.001 TRP A1730 HIS 0.023 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00343 (21454) covalent geometry : angle 0.61784 (29072) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.59640 ( 2) hydrogen bonds : bond 0.04357 ( 1084) hydrogen bonds : angle 4.28407 ( 3174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 252 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7904 (tp) cc_final: 0.7701 (tp) REVERT: A 269 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.6941 (t80) REVERT: A 327 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8316 (p) REVERT: A 330 TYR cc_start: 0.8284 (m-80) cc_final: 0.7477 (m-80) REVERT: A 366 ARG cc_start: 0.6420 (mtm180) cc_final: 0.6024 (mtp-110) REVERT: A 601 MET cc_start: 0.7459 (mtp) cc_final: 0.7092 (mtt) REVERT: A 641 LEU cc_start: 0.8431 (tt) cc_final: 0.8154 (mp) REVERT: A 811 PHE cc_start: 0.4836 (OUTLIER) cc_final: 0.4527 (t80) REVERT: A 947 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7500 (ptm160) REVERT: A 1051 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5520 (pp20) REVERT: A 1442 VAL cc_start: 0.8546 (t) cc_final: 0.8338 (t) REVERT: A 1871 MET cc_start: 0.8854 (mmt) cc_final: 0.8586 (mmt) REVERT: A 1968 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.6660 (tpm170) REVERT: A 2593 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.6174 (ptpp) REVERT: A 2637 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8001 (ttt90) REVERT: A 2836 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7806 (tm-30) outliers start: 89 outliers final: 60 residues processed: 328 average time/residue: 0.1423 time to fit residues: 73.7177 Evaluate side-chains 288 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 ARG Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1571 ARG Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 88 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 201 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 418 HIS A 450 HIS A2129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123588 restraints weight = 35793.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122881 restraints weight = 35931.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123644 restraints weight = 37533.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125409 restraints weight = 26304.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125415 restraints weight = 20071.201| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21455 Z= 0.128 Angle : 0.577 10.105 29074 Z= 0.286 Chirality : 0.040 0.309 3333 Planarity : 0.004 0.048 3710 Dihedral : 7.735 159.670 2959 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.28 % Allowed : 16.50 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2612 helix: 0.27 (0.13), residues: 1793 sheet: -0.60 (0.91), residues: 38 loop : -2.26 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2603 TYR 0.011 0.001 TYR A2649 PHE 0.019 0.001 PHE A2112 TRP 0.022 0.001 TRP A1730 HIS 0.007 0.001 HIS A2518 Details of bonding type rmsd covalent geometry : bond 0.00296 (21454) covalent geometry : angle 0.57697 (29072) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.38849 ( 2) hydrogen bonds : bond 0.03826 ( 1084) hydrogen bonds : angle 4.02608 ( 3174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 249 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7146 (tt) cc_final: 0.6937 (mp) REVERT: A 140 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6774 (m-10) REVERT: A 269 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6826 (t80) REVERT: A 327 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 330 TYR cc_start: 0.8315 (m-80) cc_final: 0.7499 (m-80) REVERT: A 366 ARG cc_start: 0.6362 (mtm180) cc_final: 0.6034 (mtp-110) REVERT: A 601 MET cc_start: 0.7285 (mtp) cc_final: 0.6934 (mtt) REVERT: A 641 LEU cc_start: 0.8395 (tt) cc_final: 0.8086 (mp) REVERT: A 734 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: A 919 LEU cc_start: 0.8482 (mm) cc_final: 0.8099 (mt) REVERT: A 1051 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5501 (pp20) REVERT: A 1249 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8501 (pp) REVERT: A 1442 VAL cc_start: 0.8566 (t) cc_final: 0.8359 (t) REVERT: A 1628 GLU cc_start: 0.6844 (mp0) cc_final: 0.6534 (mp0) REVERT: A 1871 MET cc_start: 0.8859 (mmt) cc_final: 0.8648 (mmt) REVERT: A 1968 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6625 (tpm170) REVERT: A 2389 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7338 (p0) REVERT: A 2550 MET cc_start: 0.8270 (mmm) cc_final: 0.8031 (mmm) REVERT: A 2593 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.6305 (ptpp) REVERT: A 2637 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7930 (ttt90) REVERT: A 2836 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7732 (tm-30) outliers start: 98 outliers final: 61 residues processed: 328 average time/residue: 0.1402 time to fit residues: 72.6048 Evaluate side-chains 290 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 220 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1571 ARG Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2389 ASP Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2853 SER Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 239 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 117 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124177 restraints weight = 35423.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122993 restraints weight = 33394.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124400 restraints weight = 34389.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124856 restraints weight = 22284.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125222 restraints weight = 20413.003| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21455 Z= 0.111 Angle : 0.554 10.075 29074 Z= 0.273 Chirality : 0.039 0.251 3333 Planarity : 0.004 0.047 3710 Dihedral : 7.446 159.822 2950 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.58 % Allowed : 17.59 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2612 helix: 0.53 (0.13), residues: 1802 sheet: -0.50 (0.91), residues: 38 loop : -2.11 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 336 TYR 0.009 0.001 TYR A2517 PHE 0.014 0.001 PHE A2112 TRP 0.020 0.001 TRP A 616 HIS 0.008 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00257 (21454) covalent geometry : angle 0.55379 (29072) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.27958 ( 2) hydrogen bonds : bond 0.03482 ( 1084) hydrogen bonds : angle 3.84377 ( 3174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 236 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.5296 (m-80) REVERT: A 140 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6824 (m-10) REVERT: A 269 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 330 TYR cc_start: 0.8370 (m-80) cc_final: 0.7582 (m-80) REVERT: A 366 ARG cc_start: 0.6296 (mtm180) cc_final: 0.5990 (mtm-85) REVERT: A 399 GLU cc_start: 0.6429 (pm20) cc_final: 0.6039 (pm20) REVERT: A 408 LEU cc_start: 0.8006 (tp) cc_final: 0.7723 (mp) REVERT: A 601 MET cc_start: 0.7236 (mtp) cc_final: 0.6894 (mtt) REVERT: A 641 LEU cc_start: 0.8397 (tt) cc_final: 0.8047 (mp) REVERT: A 734 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6247 (tt0) REVERT: A 786 LEU cc_start: 0.6527 (pp) cc_final: 0.5655 (mt) REVERT: A 919 LEU cc_start: 0.8646 (mm) cc_final: 0.8301 (mt) REVERT: A 1051 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.5436 (pp20) REVERT: A 1249 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8535 (pp) REVERT: A 1288 LYS cc_start: 0.8378 (mttm) cc_final: 0.8171 (tptp) REVERT: A 1442 VAL cc_start: 0.8490 (t) cc_final: 0.8289 (t) REVERT: A 1610 ILE cc_start: 0.8235 (tt) cc_final: 0.7773 (mt) REVERT: A 1628 GLU cc_start: 0.6789 (mp0) cc_final: 0.6469 (mp0) REVERT: A 1968 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.6173 (mmp-170) REVERT: A 2593 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.6523 (ptpp) REVERT: A 2637 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7928 (ttt90) REVERT: A 2836 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7746 (tm-30) outliers start: 82 outliers final: 61 residues processed: 304 average time/residue: 0.1426 time to fit residues: 68.6462 Evaluate side-chains 285 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2853 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 chunk 203 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 123 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 474 HIS A1035 GLN A1593 ASN A2290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122195 restraints weight = 35453.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120583 restraints weight = 37372.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122159 restraints weight = 36097.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122584 restraints weight = 24004.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122957 restraints weight = 22086.793| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21455 Z= 0.139 Angle : 0.576 10.672 29074 Z= 0.282 Chirality : 0.040 0.331 3333 Planarity : 0.004 0.045 3710 Dihedral : 7.306 160.273 2942 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.32 % Allowed : 17.85 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2612 helix: 0.66 (0.13), residues: 1807 sheet: -0.51 (0.90), residues: 38 loop : -2.04 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1287 TYR 0.016 0.001 TYR A2040 PHE 0.015 0.001 PHE A2112 TRP 0.027 0.001 TRP A 530 HIS 0.005 0.001 HIS A2518 Details of bonding type rmsd covalent geometry : bond 0.00334 (21454) covalent geometry : angle 0.57597 (29072) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.35006 ( 2) hydrogen bonds : bond 0.03687 ( 1084) hydrogen bonds : angle 3.85922 ( 3174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 231 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5340 (m-80) REVERT: A 140 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: A 269 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 330 TYR cc_start: 0.8432 (m-80) cc_final: 0.7672 (m-80) REVERT: A 366 ARG cc_start: 0.6371 (mtm180) cc_final: 0.6010 (mtm-85) REVERT: A 399 GLU cc_start: 0.6496 (pm20) cc_final: 0.5952 (pm20) REVERT: A 401 ASN cc_start: 0.8056 (m-40) cc_final: 0.7797 (m-40) REVERT: A 601 MET cc_start: 0.7282 (mtp) cc_final: 0.6956 (mtt) REVERT: A 641 LEU cc_start: 0.8375 (tt) cc_final: 0.8094 (mp) REVERT: A 734 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6112 (tt0) REVERT: A 786 LEU cc_start: 0.6547 (pp) cc_final: 0.5669 (mt) REVERT: A 1051 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.5436 (pp20) REVERT: A 1249 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8581 (pp) REVERT: A 1270 ASP cc_start: 0.7917 (m-30) cc_final: 0.7042 (p0) REVERT: A 1610 ILE cc_start: 0.8353 (tt) cc_final: 0.8018 (mt) REVERT: A 1628 GLU cc_start: 0.6702 (mp0) cc_final: 0.6398 (mp0) REVERT: A 1730 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.7036 (m-10) REVERT: A 1968 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.6587 (tpm170) REVERT: A 2593 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.6793 (ptpp) REVERT: A 2637 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7970 (ttt90) REVERT: A 2836 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7811 (tm-30) outliers start: 99 outliers final: 71 residues processed: 308 average time/residue: 0.1349 time to fit residues: 66.7846 Evaluate side-chains 295 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 215 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2119 MET Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2192 ILE Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2774 GLU Chi-restraints excluded: chain A residue 2853 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 5 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1161 HIS A1717 GLN ** A2518 HIS ** 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 = 0.3868 r_free = 0.3868 target = 0.149236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122773 restraints weight = 35615.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121430 restraints weight = 37776.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122372 restraints weight = 38054.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124314 restraints weight = 26552.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124560 restraints weight = 19461.855| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 21455 Z= 0.125 Angle : 0.561 9.693 29074 Z= 0.275 Chirality : 0.040 0.382 3333 Planarity : 0.004 0.046 3710 Dihedral : 7.191 161.310 2940 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.88 % Allowed : 18.46 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2612 helix: 0.80 (0.13), residues: 1815 sheet: 0.00 (0.95), residues: 33 loop : -2.00 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2603 TYR 0.019 0.001 TYR A2040 PHE 0.012 0.001 PHE A2112 TRP 0.021 0.001 TRP A 530 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00297 (21454) covalent geometry : angle 0.56054 (29072) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.26606 ( 2) hydrogen bonds : bond 0.03489 ( 1084) hydrogen bonds : angle 3.80152 ( 3174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 224 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5478 (m-80) REVERT: A 140 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6631 (m-10) REVERT: A 269 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 330 TYR cc_start: 0.8436 (m-80) cc_final: 0.7725 (m-80) REVERT: A 366 ARG cc_start: 0.6298 (mtm180) cc_final: 0.5966 (mtm-85) REVERT: A 399 GLU cc_start: 0.6550 (pm20) cc_final: 0.5963 (pm20) REVERT: A 401 ASN cc_start: 0.8077 (m-40) cc_final: 0.7796 (m-40) REVERT: A 530 TRP cc_start: 0.6013 (t-100) cc_final: 0.5220 (t60) REVERT: A 601 MET cc_start: 0.7236 (mtp) cc_final: 0.6939 (mtt) REVERT: A 641 LEU cc_start: 0.8351 (tt) cc_final: 0.8104 (mp) REVERT: A 734 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6025 (tt0) REVERT: A 786 LEU cc_start: 0.6304 (pp) cc_final: 0.5464 (mt) REVERT: A 919 LEU cc_start: 0.8443 (mm) cc_final: 0.7993 (mt) REVERT: A 1051 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.5396 (pp20) REVERT: A 1249 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8376 (pp) REVERT: A 1270 ASP cc_start: 0.7842 (m-30) cc_final: 0.7084 (p0) REVERT: A 1610 ILE cc_start: 0.8416 (tt) cc_final: 0.8115 (mt) REVERT: A 1717 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7019 (mp-120) REVERT: A 1730 TRP cc_start: 0.7689 (OUTLIER) cc_final: 0.6513 (m-10) REVERT: A 2140 MET cc_start: 0.7757 (tpt) cc_final: 0.7483 (tpt) REVERT: A 2593 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.6725 (ptpp) REVERT: A 2637 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7984 (ttt90) REVERT: A 2836 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7783 (tm-30) outliers start: 89 outliers final: 65 residues processed: 297 average time/residue: 0.1259 time to fit residues: 61.4233 Evaluate side-chains 293 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 218 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 126 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 253 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1717 GLN ** A2518 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.148144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121991 restraints weight = 35234.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120778 restraints weight = 38230.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121681 restraints weight = 38177.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123528 restraints weight = 26702.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123705 restraints weight = 19929.689| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 21455 Z= 0.129 Angle : 0.564 11.130 29074 Z= 0.277 Chirality : 0.040 0.305 3333 Planarity : 0.004 0.041 3710 Dihedral : 7.060 161.603 2938 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.62 % Allowed : 18.86 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2612 helix: 0.89 (0.13), residues: 1795 sheet: -0.02 (0.94), residues: 33 loop : -1.91 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2603 TYR 0.023 0.001 TYR A2040 PHE 0.012 0.001 PHE A2112 TRP 0.021 0.001 TRP A 616 HIS 0.005 0.001 HIS A2518 Details of bonding type rmsd covalent geometry : bond 0.00311 (21454) covalent geometry : angle 0.56367 (29072) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.26574 ( 2) hydrogen bonds : bond 0.03507 ( 1084) hydrogen bonds : angle 3.79227 ( 3174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 219 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.5459 (m-80) REVERT: A 140 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6534 (m-10) REVERT: A 269 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6919 (t80) REVERT: A 330 TYR cc_start: 0.8456 (m-80) cc_final: 0.7729 (m-80) REVERT: A 358 TYR cc_start: 0.6579 (OUTLIER) cc_final: 0.5219 (t80) REVERT: A 366 ARG cc_start: 0.6380 (mtm180) cc_final: 0.5852 (mtm-85) REVERT: A 401 ASN cc_start: 0.7986 (m-40) cc_final: 0.7731 (m-40) REVERT: A 530 TRP cc_start: 0.5834 (t-100) cc_final: 0.5244 (t60) REVERT: A 601 MET cc_start: 0.7219 (mtp) cc_final: 0.6938 (mtt) REVERT: A 641 LEU cc_start: 0.8328 (tt) cc_final: 0.8106 (mp) REVERT: A 734 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6093 (tt0) REVERT: A 919 LEU cc_start: 0.8513 (mm) cc_final: 0.8036 (mt) REVERT: A 1051 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.5414 (pp20) REVERT: A 1249 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 1270 ASP cc_start: 0.7774 (m-30) cc_final: 0.7127 (p0) REVERT: A 1610 ILE cc_start: 0.8455 (tt) cc_final: 0.8178 (mt) REVERT: A 1717 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7930 (mp-120) REVERT: A 1730 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: A 2140 MET cc_start: 0.7775 (tpt) cc_final: 0.7471 (tpt) REVERT: A 2593 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.6862 (ptpp) REVERT: A 2637 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8005 (ttt90) REVERT: A 2836 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 83 outliers final: 66 residues processed: 286 average time/residue: 0.1319 time to fit residues: 61.7008 Evaluate side-chains 287 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2230 ILE Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2531 SER Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2651 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2705 THR Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2801 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 220 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 206 optimal weight: 0.0980 chunk 167 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A1717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125021 restraints weight = 35471.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123723 restraints weight = 46224.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124654 restraints weight = 42359.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126196 restraints weight = 29027.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126288 restraints weight = 23271.925| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 21455 Z= 0.112 Angle : 0.551 11.872 29074 Z= 0.270 Chirality : 0.039 0.309 3333 Planarity : 0.004 0.041 3710 Dihedral : 6.994 161.956 2938 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.40 % Allowed : 19.38 % Favored : 77.22 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2612 helix: 1.01 (0.13), residues: 1805 sheet: 0.07 (0.94), residues: 33 loop : -1.86 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2603 TYR 0.021 0.001 TYR A2040 PHE 0.010 0.001 PHE A2112 TRP 0.020 0.001 TRP A 616 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00268 (21454) covalent geometry : angle 0.55083 (29072) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.24290 ( 2) hydrogen bonds : bond 0.03300 ( 1084) hydrogen bonds : angle 3.71017 ( 3174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5867 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: A 140 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6401 (m-10) REVERT: A 269 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 330 TYR cc_start: 0.8424 (m-80) cc_final: 0.7715 (m-80) REVERT: A 358 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.5320 (t80) REVERT: A 366 ARG cc_start: 0.6302 (mtm180) cc_final: 0.5877 (mtm-85) REVERT: A 399 GLU cc_start: 0.6416 (pm20) cc_final: 0.5700 (pm20) REVERT: A 401 ASN cc_start: 0.8074 (m-40) cc_final: 0.7833 (m-40) REVERT: A 530 TRP cc_start: 0.5691 (t-100) cc_final: 0.5050 (t60) REVERT: A 601 MET cc_start: 0.7213 (mtp) cc_final: 0.6958 (mtt) REVERT: A 734 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5696 (tt0) REVERT: A 1051 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.5450 (pp20) REVERT: A 1249 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8456 (pp) REVERT: A 1270 ASP cc_start: 0.7610 (m-30) cc_final: 0.7139 (p0) REVERT: A 1610 ILE cc_start: 0.8441 (tt) cc_final: 0.8195 (mt) REVERT: A 1717 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7493 (mp-120) REVERT: A 1730 TRP cc_start: 0.7759 (OUTLIER) cc_final: 0.7076 (m-10) REVERT: A 2140 MET cc_start: 0.7777 (tpt) cc_final: 0.7487 (tpt) REVERT: A 2238 LYS cc_start: 0.6791 (pptt) cc_final: 0.6322 (pptt) REVERT: A 2593 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.6791 (ptpp) REVERT: A 2637 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7987 (ttt90) REVERT: A 2836 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7753 (tm-30) outliers start: 78 outliers final: 60 residues processed: 291 average time/residue: 0.1305 time to fit residues: 61.1635 Evaluate side-chains 286 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2148 ARG Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2531 SER Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2593 LYS Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 244 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 92 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 GLN A1512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123390 restraints weight = 35258.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122859 restraints weight = 38852.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123708 restraints weight = 37998.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125494 restraints weight = 26197.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125533 restraints weight = 19984.109| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 21455 Z= 0.114 Angle : 0.555 11.003 29074 Z= 0.272 Chirality : 0.039 0.276 3333 Planarity : 0.004 0.041 3710 Dihedral : 6.952 162.024 2937 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.27 % Allowed : 19.77 % Favored : 76.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2612 helix: 1.08 (0.13), residues: 1806 sheet: 0.08 (0.93), residues: 33 loop : -1.80 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 620 TYR 0.020 0.001 TYR A2040 PHE 0.010 0.001 PHE A2112 TRP 0.023 0.001 TRP A 616 HIS 0.004 0.001 HIS A2518 Details of bonding type rmsd covalent geometry : bond 0.00277 (21454) covalent geometry : angle 0.55540 (29072) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.24065 ( 2) hydrogen bonds : bond 0.03278 ( 1084) hydrogen bonds : angle 3.70125 ( 3174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 220 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.5457 (m-80) REVERT: A 140 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: A 269 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6935 (t80) REVERT: A 330 TYR cc_start: 0.8451 (m-80) cc_final: 0.7783 (m-80) REVERT: A 358 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5265 (t80) REVERT: A 366 ARG cc_start: 0.6294 (mtm180) cc_final: 0.5854 (mtm-85) REVERT: A 399 GLU cc_start: 0.6478 (pm20) cc_final: 0.5788 (pm20) REVERT: A 401 ASN cc_start: 0.8078 (m-40) cc_final: 0.7822 (m-40) REVERT: A 530 TRP cc_start: 0.5758 (t-100) cc_final: 0.5001 (t60) REVERT: A 601 MET cc_start: 0.7208 (mtp) cc_final: 0.6942 (mtt) REVERT: A 734 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5838 (tt0) REVERT: A 1051 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.5440 (pp20) REVERT: A 1249 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8478 (pp) REVERT: A 1270 ASP cc_start: 0.7567 (m-30) cc_final: 0.7115 (p0) REVERT: A 1502 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7702 (mmtp) REVERT: A 1610 ILE cc_start: 0.8461 (tt) cc_final: 0.8234 (mt) REVERT: A 1730 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: A 2140 MET cc_start: 0.7795 (tpt) cc_final: 0.7502 (tpt) REVERT: A 2238 LYS cc_start: 0.6814 (pptt) cc_final: 0.6293 (pptt) REVERT: A 2637 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7988 (ttt90) REVERT: A 2836 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7789 (tm-30) outliers start: 75 outliers final: 57 residues processed: 279 average time/residue: 0.1205 time to fit residues: 55.4870 Evaluate side-chains 277 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1527 PHE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1654 GLU Chi-restraints excluded: chain A residue 1717 GLN Chi-restraints excluded: chain A residue 1730 TRP Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1758 GLU Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2137 THR Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2261 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2531 SER Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2565 SER Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2751 MET Chi-restraints excluded: chain A residue 2752 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 97 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 235 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2844 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122377 restraints weight = 35477.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121519 restraints weight = 39223.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122361 restraints weight = 38854.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124049 restraints weight = 27030.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124145 restraints weight = 20960.172| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 21455 Z= 0.126 Angle : 0.571 12.723 29074 Z= 0.277 Chirality : 0.040 0.268 3333 Planarity : 0.004 0.040 3710 Dihedral : 6.868 162.424 2935 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.32 % Allowed : 19.60 % Favored : 77.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2612 helix: 1.13 (0.13), residues: 1804 sheet: -0.19 (0.88), residues: 35 loop : -1.84 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 620 TYR 0.019 0.001 TYR A2040 PHE 0.012 0.001 PHE A2112 TRP 0.021 0.001 TRP A 616 HIS 0.005 0.001 HIS A2518 Details of bonding type rmsd covalent geometry : bond 0.00310 (21454) covalent geometry : angle 0.57123 (29072) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.25954 ( 2) hydrogen bonds : bond 0.03422 ( 1084) hydrogen bonds : angle 3.70850 ( 3174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3131.38 seconds wall clock time: 54 minutes 57.12 seconds (3297.12 seconds total)