Starting phenix.real_space_refine on Fri Feb 6 01:03:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1l_63575/02_2026/9m1l_63575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1l_63575/02_2026/9m1l_63575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1l_63575/02_2026/9m1l_63575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1l_63575/02_2026/9m1l_63575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1l_63575/02_2026/9m1l_63575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1l_63575/02_2026/9m1l_63575.map" } resolution = 2.55 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= 0.001 sd= 0.026 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 9 5.49 5 Mg 3 5.21 5 S 123 5.16 5 C 13337 2.51 5 N 3657 2.21 5 O 3961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21090 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8680 Classifications: {'peptide': 1107} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1060} Chain breaks: 2 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1467 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "E" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4040 Classifications: {'peptide': 510} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 483} Chain breaks: 1 Chain: "a" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3424 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 417} Chain: "b" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3380 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.21, per 1000 atoms: 0.20 Number of scatterers: 21090 At special positions: 0 Unit cell: (154.429, 131.119, 153.457, 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 123 16.00 P 9 15.00 Mg 3 11.99 O 3961 8.00 N 3657 7.00 C 13337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4986 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 12 sheets defined 55.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'D' and resid 32 through 42 removed outlier: 4.490A pdb=" N ALA D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.586A pdb=" N ARG D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.570A pdb=" N LEU D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D 75 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.908A pdb=" N LEU D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 removed outlier: 3.523A pdb=" N VAL D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.506A pdb=" N VAL D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.549A pdb=" N ARG D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.790A pdb=" N LEU D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 171 " --> pdb=" O PHE D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 171' Processing helix chain 'D' and resid 184 through 197 Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.642A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'D' and resid 243 through 263 removed outlier: 3.684A pdb=" N VAL D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 282 removed outlier: 4.145A pdb=" N VAL D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 removed outlier: 3.512A pdb=" N PHE D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 367 removed outlier: 4.090A pdb=" N GLU D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 363 " --> pdb=" O GLU D 359 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 Processing helix chain 'D' and resid 373 through 389 removed outlier: 3.690A pdb=" N ARG D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS D 382 " --> pdb=" O TRP D 378 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.592A pdb=" N ASP D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.557A pdb=" N TRP D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.643A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 475 removed outlier: 4.123A pdb=" N ALA D 475 " --> pdb=" O CYS D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 498 Proline residue: D 485 - end of helix removed outlier: 4.276A pdb=" N THR D 488 " --> pdb=" O LYS D 484 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA D 489 " --> pdb=" O PRO D 485 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 492 " --> pdb=" O THR D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 521 Processing helix chain 'D' and resid 526 through 534 removed outlier: 3.565A pdb=" N LEU D 531 " --> pdb=" O GLY D 527 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 533 " --> pdb=" O ASP D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 571 through 574 Processing helix chain 'D' and resid 577 through 594 removed outlier: 3.948A pdb=" N ALA D 584 " --> pdb=" O ARG D 580 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN D 592 " --> pdb=" O HIS D 588 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN D 593 " --> pdb=" O ASN D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 601 Processing helix chain 'D' and resid 601 through 610 removed outlier: 4.190A pdb=" N ARG D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 639 removed outlier: 3.538A pdb=" N ARG D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 646 removed outlier: 3.650A pdb=" N ASP D 645 " --> pdb=" O PRO D 642 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS D 646 " --> pdb=" O VAL D 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 642 through 646' Processing helix chain 'D' and resid 648 through 666 removed outlier: 3.524A pdb=" N LYS D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 689 removed outlier: 4.425A pdb=" N LEU D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 3.879A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'D' and resid 721 through 738 removed outlier: 3.738A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 730 " --> pdb=" O LYS D 726 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D 731 " --> pdb=" O ASP D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 removed outlier: 3.761A pdb=" N GLU D 755 " --> pdb=" O ALA D 751 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 757 " --> pdb=" O GLN D 753 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR D 758 " --> pdb=" O GLU D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 781 removed outlier: 3.808A pdb=" N ARG D 772 " --> pdb=" O GLU D 768 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU D 777 " --> pdb=" O CYS D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 803 removed outlier: 3.648A pdb=" N VAL D 801 " --> pdb=" O GLY D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.667A pdb=" N ARG D 815 " --> pdb=" O PHE D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 856 removed outlier: 3.553A pdb=" N CYS D 855 " --> pdb=" O ALA D 851 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET D 856 " --> pdb=" O LEU D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 888 removed outlier: 3.983A pdb=" N VAL D 871 " --> pdb=" O VAL D 867 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 874 " --> pdb=" O TRP D 870 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 879 " --> pdb=" O ALA D 875 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 882 " --> pdb=" O SER D 878 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR D 883 " --> pdb=" O LEU D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 894 removed outlier: 6.361A pdb=" N GLU D 892 " --> pdb=" O SER D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 910 Processing helix chain 'D' and resid 915 through 931 Processing helix chain 'D' and resid 941 through 949 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 961 through 964 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 975 Processing helix chain 'D' and resid 979 through 990 removed outlier: 3.936A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1010 removed outlier: 3.515A pdb=" N TYR D1008 " --> pdb=" O SER D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1013 No H-bonds generated for 'chain 'D' and resid 1011 through 1013' Processing helix chain 'D' and resid 1015 through 1033 Processing helix chain 'D' and resid 1039 through 1054 removed outlier: 3.526A pdb=" N HIS D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D1054 " --> pdb=" O VAL D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1062 removed outlier: 3.577A pdb=" N THR D1061 " --> pdb=" O ILE D1058 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D1062 " --> pdb=" O PHE D1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1058 through 1062' Processing helix chain 'D' and resid 1065 through 1079 Processing helix chain 'D' and resid 1084 through 1098 removed outlier: 3.734A pdb=" N SER D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1118 removed outlier: 3.567A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS D1118 " --> pdb=" O CYS D1114 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 Processing helix chain 'D' and resid 1144 through 1155 removed outlier: 4.183A pdb=" N ASP D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1179 removed outlier: 4.471A pdb=" N GLU D1169 " --> pdb=" O ALA D1165 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.785A pdb=" N LYS G 35 " --> pdb=" O THR G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 75 removed outlier: 3.995A pdb=" N SER G 75 " --> pdb=" O LYS G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 80 removed outlier: 3.821A pdb=" N ASN G 79 " --> pdb=" O TYR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 164 through 178 removed outlier: 3.762A pdb=" N GLY G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.952A pdb=" N GLN E 125 " --> pdb=" O LYS E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 129 removed outlier: 3.867A pdb=" N LEU E 129 " --> pdb=" O LEU E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 126 through 129' Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.973A pdb=" N VAL E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 225 removed outlier: 3.646A pdb=" N LEU E 222 " --> pdb=" O TRP E 218 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 273 removed outlier: 3.915A pdb=" N LEU E 272 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 273 " --> pdb=" O GLN E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.763A pdb=" N GLU E 329 " --> pdb=" O PHE E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 removed outlier: 3.684A pdb=" N LEU E 357 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.648A pdb=" N PHE E 389 " --> pdb=" O TYR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 396 Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 440 through 444 removed outlier: 3.822A pdb=" N GLN E 444 " --> pdb=" O MET E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 440 through 444' Processing helix chain 'E' and resid 470 through 483 removed outlier: 3.521A pdb=" N VAL E 474 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 29 removed outlier: 3.837A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 51 removed outlier: 3.906A pdb=" N THR a 51 " --> pdb=" O SER a 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 48 through 51' Processing helix chain 'a' and resid 71 through 80 removed outlier: 4.341A pdb=" N ILE a 75 " --> pdb=" O GLU a 71 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 111 through 129 removed outlier: 3.696A pdb=" N ILE a 115 " --> pdb=" O GLY a 111 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP a 116 " --> pdb=" O LYS a 112 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU a 117 " --> pdb=" O GLU a 113 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP a 120 " --> pdb=" O ASP a 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS a 124 " --> pdb=" O ASP a 120 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU a 125 " --> pdb=" O ARG a 121 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN a 128 " --> pdb=" O LYS a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 161 removed outlier: 3.934A pdb=" N THR a 150 " --> pdb=" O GLY a 146 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP a 160 " --> pdb=" O ARG a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 194 removed outlier: 3.521A pdb=" N HIS a 192 " --> pdb=" O ILE a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 216 Processing helix chain 'a' and resid 223 through 244 removed outlier: 3.633A pdb=" N GLN a 233 " --> pdb=" O ARG a 229 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE a 234 " --> pdb=" O LEU a 230 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU a 242 " --> pdb=" O ILE a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 259 removed outlier: 3.714A pdb=" N PHE a 255 " --> pdb=" O ASP a 251 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN a 256 " --> pdb=" O LEU a 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR a 257 " --> pdb=" O THR a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 295 removed outlier: 3.538A pdb=" N CYS a 295 " --> pdb=" O ILE a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 310 Processing helix chain 'a' and resid 324 through 338 removed outlier: 3.750A pdb=" N ALA a 330 " --> pdb=" O LYS a 326 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS a 336 " --> pdb=" O ILE a 332 " (cutoff:3.500A) Processing helix chain 'a' and resid 384 through 401 removed outlier: 3.620A pdb=" N TRP a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU a 391 " --> pdb=" O ALA a 387 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS a 401 " --> pdb=" O LEU a 397 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 410 Processing helix chain 'a' and resid 414 through 436 removed outlier: 4.472A pdb=" N PHE a 418 " --> pdb=" O GLU a 414 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY a 436 " --> pdb=" O TYR a 432 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 Processing helix chain 'b' and resid 40 through 44 Processing helix chain 'b' and resid 46 through 49 Processing helix chain 'b' and resid 71 through 78 Processing helix chain 'b' and resid 112 through 126 removed outlier: 4.167A pdb=" N SER b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 159 removed outlier: 3.769A pdb=" N THR b 149 " --> pdb=" O SER b 145 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU b 157 " --> pdb=" O SER b 153 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU b 158 " --> pdb=" O LYS b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 195 removed outlier: 3.863A pdb=" N ASN b 184 " --> pdb=" O VAL b 180 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU b 194 " --> pdb=" O HIS b 190 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN b 195 " --> pdb=" O GLN b 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 203 through 214 removed outlier: 3.823A pdb=" N LEU b 207 " --> pdb=" O ASP b 203 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.739A pdb=" N LEU b 225 " --> pdb=" O THR b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 285 through 294 removed outlier: 3.913A pdb=" N PHE b 294 " --> pdb=" O THR b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 331 Processing helix chain 'b' and resid 374 through 391 removed outlier: 3.673A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE b 381 " --> pdb=" O LEU b 377 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN b 384 " --> pdb=" O ARG b 380 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET b 388 " --> pdb=" O GLN b 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG b 391 " --> pdb=" O ALA b 387 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 402 removed outlier: 3.626A pdb=" N GLU b 401 " --> pdb=" O TRP b 397 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY b 402 " --> pdb=" O TYR b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 427 removed outlier: 3.714A pdb=" N PHE b 408 " --> pdb=" O ASP b 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AA2, first strand: chain 'G' and resid 50 through 57 removed outlier: 6.690A pdb=" N LEU G 17 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TRP G 65 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU G 19 " --> pdb=" O TRP G 65 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL G 67 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET G 21 " --> pdb=" O VAL G 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 13 through 16 removed outlier: 6.286A pdb=" N VAL E 23 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU E 40 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE E 25 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 105 through 106 removed outlier: 7.489A pdb=" N VAL a 353 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU E 112 " --> pdb=" O VAL a 353 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE a 355 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA a 314 " --> pdb=" O ASN a 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'E' and resid 183 through 185 removed outlier: 7.016A pdb=" N LEU E 184 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU E 209 " --> pdb=" O TYR E 235 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 234 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU E 257 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU E 282 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU E 312 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 337 " --> pdb=" O THR E 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 463 through 466 removed outlier: 3.557A pdb=" N ILE E 503 " --> pdb=" O TYR E 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 65 through 68 removed outlier: 8.118A pdb=" N VAL a 66 " --> pdb=" O CYS a 4 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER a 6 " --> pdb=" O VAL a 66 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL a 68 " --> pdb=" O SER a 6 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS a 8 " --> pdb=" O VAL a 68 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU a 3 " --> pdb=" O LEU a 132 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY a 134 " --> pdb=" O GLU a 3 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE a 5 " --> pdb=" O GLY a 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'b' and resid 90 through 92 removed outlier: 7.768A pdb=" N GLU b 3 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE b 133 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL b 5 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU b 135 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE b 7 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE b 163 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN b 165 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET b 164 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR b 200 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR b 166 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE b 265 " --> pdb=" O SER b 371 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER b 371 " --> pdb=" O PHE b 265 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE b 367 " --> pdb=" O GLY b 269 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR b 312 " --> pdb=" O ASN b 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 90 through 92 removed outlier: 7.768A pdb=" N GLU b 3 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE b 133 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL b 5 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU b 135 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE b 7 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE b 163 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN b 165 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET b 164 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR b 200 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR b 166 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE b 265 " --> pdb=" O SER b 371 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER b 371 " --> pdb=" O PHE b 265 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE b 367 " --> pdb=" O GLY b 269 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA b 314 " --> pdb=" O ILE b 368 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA b 315 " --> pdb=" O ALA b 352 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N CYS b 354 " --> pdb=" O ALA b 315 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE b 317 " --> pdb=" O CYS b 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 51 through 53 947 hydrogen bonds defined for protein. 2748 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: 3.49 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3556 1.32 - 1.44: 5506 1.44 - 1.56: 12256 1.56 - 1.69: 15 1.69 - 1.81: 183 Bond restraints: 21516 Sorted by residual: bond pdb=" C MET D 570 " pdb=" N LYS D 571 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.27e-02 6.20e+03 2.33e+01 bond pdb=" N VAL D 939 " pdb=" CA VAL D 939 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.60e-03 1.73e+04 2.00e+01 bond pdb=" N VAL D 220 " pdb=" CA VAL D 220 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.69e+01 bond pdb=" N LYS E 109 " pdb=" CA LYS E 109 " ideal model delta sigma weight residual 1.453 1.491 -0.037 9.20e-03 1.18e+04 1.64e+01 bond pdb=" C TRP G 77 " pdb=" N ARG G 78 " ideal model delta sigma weight residual 1.332 1.390 -0.059 1.52e-02 4.33e+03 1.48e+01 ... (remaining 21511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 28915 3.62 - 7.24: 238 7.24 - 10.85: 24 10.85 - 14.47: 1 14.47 - 18.09: 4 Bond angle restraints: 29182 Sorted by residual: angle pdb=" PA GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PB GTP b1500 " ideal model delta sigma weight residual 120.50 138.59 -18.09 3.00e+00 1.11e-01 3.64e+01 angle pdb=" PB GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 120.50 137.64 -17.14 3.00e+00 1.11e-01 3.27e+01 angle pdb=" PB GTP G1500 " pdb=" O3B GTP G1500 " pdb=" PG GTP G1500 " ideal model delta sigma weight residual 120.50 135.71 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N TRP E 322 " pdb=" CA TRP E 322 " pdb=" C TRP E 322 " ideal model delta sigma weight residual 113.02 107.03 5.99 1.20e+00 6.94e-01 2.49e+01 angle pdb=" C ARG b 318 " pdb=" CA ARG b 318 " pdb=" CB ARG b 318 " ideal model delta sigma weight residual 110.14 118.02 -7.88 1.60e+00 3.91e-01 2.42e+01 ... (remaining 29177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 12733 36.00 - 71.99: 212 71.99 - 107.99: 15 107.99 - 143.99: 6 143.99 - 179.98: 6 Dihedral angle restraints: 12972 sinusoidal: 5252 harmonic: 7720 Sorted by residual: dihedral pdb=" O5' GTP G1500 " pdb=" O3A GTP G1500 " pdb=" PA GTP G1500 " pdb=" PB GTP G1500 " ideal model delta sinusoidal sigma weight residual 274.12 94.14 179.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP a1500 " pdb=" O5' GTP a1500 " pdb=" PA GTP a1500 " pdb=" O3A GTP a1500 " ideal model delta sinusoidal sigma weight residual 69.27 -106.15 175.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP G1500 " pdb=" C1' GTP G1500 " pdb=" N9 GTP G1500 " pdb=" O4' GTP G1500 " ideal model delta sinusoidal sigma weight residual 104.59 -65.54 170.14 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 12969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2554 0.050 - 0.101: 486 0.101 - 0.151: 208 0.151 - 0.202: 50 0.202 - 0.252: 3 Chirality restraints: 3301 Sorted by residual: chirality pdb=" CB VAL b 293 " pdb=" CA VAL b 293 " pdb=" CG1 VAL b 293 " pdb=" CG2 VAL b 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA VAL b 293 " pdb=" N VAL b 293 " pdb=" C VAL b 293 " pdb=" CB VAL b 293 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA VAL b 91 " pdb=" N VAL b 91 " pdb=" C VAL b 91 " pdb=" CB VAL b 91 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3298 not shown) Planarity restraints: 3757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN b 291 " 0.028 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C GLN b 291 " -0.093 2.00e-02 2.50e+03 pdb=" O GLN b 291 " 0.034 2.00e-02 2.50e+03 pdb=" N GLN b 292 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 142 " -0.021 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C GLY b 142 " 0.076 2.00e-02 2.50e+03 pdb=" O GLY b 142 " -0.028 2.00e-02 2.50e+03 pdb=" N THR b 143 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 144 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C GLY b 144 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY b 144 " -0.016 2.00e-02 2.50e+03 pdb=" N SER b 145 " -0.015 2.00e-02 2.50e+03 ... (remaining 3754 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5462 2.81 - 3.33: 20875 3.33 - 3.86: 33172 3.86 - 4.38: 41352 4.38 - 4.90: 68742 Nonbonded interactions: 169603 Sorted by model distance: nonbonded pdb=" O1B GTP G1500 " pdb="MG MG G1501 " model vdw 2.288 2.170 nonbonded pdb=" O1B GTP a1500 " pdb="MG MG a1501 " model vdw 2.385 2.170 nonbonded pdb=" O2B GTP b1500 " pdb="MG MG b1501 " model vdw 2.471 2.170 nonbonded pdb=" O TRP E 322 " pdb=" OD1 ASN E 326 " model vdw 2.483 3.040 nonbonded pdb=" OE1 GLN b 15 " pdb=" O6 GTP b1500 " model vdw 2.532 3.040 ... (remaining 169598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.830 Find NCS groups from input model: 0.110 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 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 : 0.006 0.066 21516 Z= 0.415 Angle : 0.842 18.090 29182 Z= 0.562 Chirality : 0.050 0.252 3301 Planarity : 0.003 0.054 3757 Dihedral : 14.763 179.982 7986 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: -2.62 (0.15), residues: 2654 helix: -1.10 (0.14), residues: 1337 sheet: -2.14 (0.31), residues: 227 loop : -2.36 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 318 TYR 0.012 0.000 TYR b 106 PHE 0.029 0.001 PHE b 90 TRP 0.017 0.001 TRP b 344 HIS 0.004 0.000 HIS b 137 Details of bonding type rmsd covalent geometry : bond 0.00573 (21516) covalent geometry : angle 0.84232 (29182) hydrogen bonds : bond 0.20472 ( 936) hydrogen bonds : angle 6.68171 ( 2748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 715 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.6556 (tt0) cc_final: 0.6279 (tt0) REVERT: D 130 GLU cc_start: 0.5859 (mt-10) cc_final: 0.5645 (mt-10) REVERT: D 165 PHE cc_start: 0.6119 (m-80) cc_final: 0.5642 (m-80) REVERT: D 235 ASN cc_start: 0.5979 (m-40) cc_final: 0.5639 (m-40) REVERT: D 295 LYS cc_start: 0.5854 (tttt) cc_final: 0.5593 (tttm) REVERT: D 360 ARG cc_start: 0.5555 (mmm160) cc_final: 0.5274 (mmm160) REVERT: D 397 ASP cc_start: 0.5800 (m-30) cc_final: 0.5562 (t70) REVERT: D 398 ASP cc_start: 0.6008 (m-30) cc_final: 0.5628 (m-30) REVERT: D 446 LYS cc_start: 0.6720 (mmmt) cc_final: 0.6308 (mmmt) REVERT: D 499 VAL cc_start: 0.6925 (t) cc_final: 0.6656 (m) REVERT: D 541 ASN cc_start: 0.6215 (t0) cc_final: 0.5660 (t0) REVERT: D 565 ASP cc_start: 0.6523 (t70) cc_final: 0.6139 (t70) REVERT: D 596 GLU cc_start: 0.6268 (tt0) cc_final: 0.5991 (tt0) REVERT: D 614 ASP cc_start: 0.6313 (t0) cc_final: 0.6047 (t70) REVERT: D 665 ARG cc_start: 0.7283 (mpt-90) cc_final: 0.7053 (mtt90) REVERT: D 749 ASP cc_start: 0.5787 (t0) cc_final: 0.5435 (t0) REVERT: D 763 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5715 (mm-30) REVERT: D 779 LEU cc_start: 0.6260 (tp) cc_final: 0.6017 (tp) REVERT: D 847 GLN cc_start: 0.6678 (mt0) cc_final: 0.6050 (mp10) REVERT: D 864 ARG cc_start: 0.6344 (mtm-85) cc_final: 0.5975 (mtm110) REVERT: D 903 MET cc_start: 0.6066 (tpt) cc_final: 0.5399 (mmm) REVERT: D 925 PHE cc_start: 0.5421 (t80) cc_final: 0.4796 (t80) REVERT: D 1002 THR cc_start: 0.6545 (m) cc_final: 0.6006 (p) REVERT: D 1028 GLN cc_start: 0.6487 (tp40) cc_final: 0.6096 (tp40) REVERT: D 1086 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6662 (tm-30) REVERT: G 15 ARG cc_start: 0.6886 (ttm110) cc_final: 0.6167 (ttm110) REVERT: G 61 LYS cc_start: 0.6500 (ttmt) cc_final: 0.6214 (tttt) REVERT: G 139 ARG cc_start: 0.5881 (ttt180) cc_final: 0.5555 (ttt180) REVERT: E 114 ILE cc_start: 0.6658 (tt) cc_final: 0.6384 (mt) REVERT: E 122 GLN cc_start: 0.5595 (mm-40) cc_final: 0.5309 (mm-40) REVERT: E 133 SER cc_start: 0.7597 (t) cc_final: 0.7372 (t) REVERT: E 157 LYS cc_start: 0.6618 (mttt) cc_final: 0.6402 (mttp) REVERT: E 159 ASP cc_start: 0.7418 (t0) cc_final: 0.7113 (t0) REVERT: E 161 SER cc_start: 0.6737 (p) cc_final: 0.6355 (p) REVERT: E 179 ARG cc_start: 0.6499 (mmt180) cc_final: 0.6149 (mmt180) REVERT: E 193 PHE cc_start: 0.6549 (m-80) cc_final: 0.6255 (m-80) REVERT: E 235 TYR cc_start: 0.7171 (m-80) cc_final: 0.6952 (m-80) REVERT: E 246 ARG cc_start: 0.6788 (ptm160) cc_final: 0.6180 (ptm160) REVERT: E 278 ARG cc_start: 0.6589 (mtt180) cc_final: 0.6316 (mtt180) REVERT: E 308 SER cc_start: 0.5782 (p) cc_final: 0.5355 (t) REVERT: E 327 GLU cc_start: 0.5725 (mm-30) cc_final: 0.4849 (mm-30) REVERT: E 330 LYS cc_start: 0.5931 (mttt) cc_final: 0.5625 (mtmm) REVERT: E 379 ARG cc_start: 0.5587 (ttt90) cc_final: 0.5209 (ttt90) REVERT: E 444 GLN cc_start: 0.7216 (tt0) cc_final: 0.6973 (tt0) REVERT: E 480 ARG cc_start: 0.6125 (mtt-85) cc_final: 0.5924 (mtt90) REVERT: E 483 LYS cc_start: 0.7358 (mmtm) cc_final: 0.7057 (mmtm) REVERT: E 490 LEU cc_start: 0.7381 (mt) cc_final: 0.7107 (mm) REVERT: E 492 SER cc_start: 0.7636 (p) cc_final: 0.7257 (t) REVERT: E 503 ILE cc_start: 0.5645 (mt) cc_final: 0.5295 (mt) REVERT: E 508 ASP cc_start: 0.6798 (m-30) cc_final: 0.6555 (m-30) REVERT: a 3 GLU cc_start: 0.7426 (mp0) cc_final: 0.5916 (mp0) REVERT: a 77 GLU cc_start: 0.5637 (tp30) cc_final: 0.5190 (tp30) REVERT: a 112 LYS cc_start: 0.7466 (ttpp) cc_final: 0.7027 (ttpp) REVERT: a 113 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6735 (mt-10) REVERT: a 128 GLN cc_start: 0.6627 (tm-30) cc_final: 0.6386 (tm-30) REVERT: a 194 THR cc_start: 0.7584 (p) cc_final: 0.7230 (t) REVERT: a 196 GLU cc_start: 0.6281 (pm20) cc_final: 0.5778 (pm20) REVERT: a 202 PHE cc_start: 0.7119 (m-80) cc_final: 0.6743 (m-80) REVERT: a 210 TYR cc_start: 0.6984 (t80) cc_final: 0.6608 (t80) REVERT: a 211 ASP cc_start: 0.7086 (m-30) cc_final: 0.6770 (m-30) REVERT: a 304 LYS cc_start: 0.7034 (mttt) cc_final: 0.6790 (mttt) REVERT: a 386 GLU cc_start: 0.5947 (mp0) cc_final: 0.5514 (mp0) REVERT: a 423 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6557 (mm-30) REVERT: a 424 ASP cc_start: 0.6996 (t0) cc_final: 0.6772 (t70) REVERT: b 86 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7446 (mtp85) outliers start: 1 outliers final: 4 residues processed: 716 average time/residue: 0.6592 time to fit residues: 532.7550 Evaluate side-chains 571 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 567 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain b residue 256 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0000 chunk 111 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 GLN D 566 HIS D 588 HIS ** D 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 GLN D 666 GLN D 920 HIS G 37 ASN E 364 GLN E 454 HIS ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 HIS a 91 GLN a 107 HIS ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 ASN a 216 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 GLN b 83 GLN b 94 GLN b 131 GLN b 165 ASN b 204 ASN b 256 ASN b 298 ASN b 329 GLN b 370 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140281 restraints weight = 27485.743| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.88 r_work: 0.3697 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21516 Z= 0.152 Angle : 0.578 7.594 29182 Z= 0.290 Chirality : 0.043 0.154 3301 Planarity : 0.005 0.052 3757 Dihedral : 10.000 167.036 2940 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.27 % Allowed : 14.24 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: -1.03 (0.16), residues: 2654 helix: 0.23 (0.14), residues: 1345 sheet: -1.55 (0.29), residues: 245 loop : -1.58 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 123 TYR 0.018 0.002 TYR E 311 PHE 0.020 0.002 PHE b 367 TRP 0.025 0.002 TRP G 77 HIS 0.008 0.001 HIS b 137 Details of bonding type rmsd covalent geometry : bond 0.00355 (21516) covalent geometry : angle 0.57818 (29182) hydrogen bonds : bond 0.03920 ( 936) hydrogen bonds : angle 3.89346 ( 2748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 649 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: D 91 ASP cc_start: 0.6340 (t0) cc_final: 0.6057 (t0) REVERT: D 225 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7184 (ttp) REVERT: D 398 ASP cc_start: 0.7500 (m-30) cc_final: 0.7239 (m-30) REVERT: D 416 TRP cc_start: 0.8160 (m100) cc_final: 0.7825 (m100) REVERT: D 429 ARG cc_start: 0.8248 (mtt90) cc_final: 0.8023 (mtt90) REVERT: D 452 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6716 (mm-30) REVERT: D 596 GLU cc_start: 0.7087 (tt0) cc_final: 0.6874 (tt0) REVERT: D 725 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7863 (mmt) REVERT: D 736 LEU cc_start: 0.7498 (tp) cc_final: 0.7290 (tt) REVERT: D 759 GLN cc_start: 0.7601 (tt0) cc_final: 0.7395 (tt0) REVERT: D 859 TYR cc_start: 0.8268 (m-80) cc_final: 0.8010 (m-80) REVERT: D 903 MET cc_start: 0.8343 (tpt) cc_final: 0.7997 (mmm) REVERT: D 1136 LEU cc_start: 0.8506 (mt) cc_final: 0.8202 (mp) REVERT: G 15 ARG cc_start: 0.7696 (ttm110) cc_final: 0.7384 (ttm110) REVERT: G 139 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7940 (ttt180) REVERT: G 140 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7639 (mt-10) REVERT: G 175 ASP cc_start: 0.7804 (t70) cc_final: 0.7597 (t0) REVERT: E 122 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6368 (mm-40) REVERT: E 177 GLN cc_start: 0.6721 (mt0) cc_final: 0.6147 (mt0) REVERT: E 213 GLN cc_start: 0.8100 (mt0) cc_final: 0.7878 (mt0) REVERT: E 321 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7256 (mm-40) REVERT: E 327 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6910 (mm-30) REVERT: E 330 LYS cc_start: 0.7651 (mttt) cc_final: 0.7115 (mtmt) REVERT: E 379 ARG cc_start: 0.6521 (ttt90) cc_final: 0.6032 (ttt90) REVERT: E 387 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8031 (ttpp) REVERT: E 429 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6224 (mm-30) REVERT: E 473 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7756 (mmtt) REVERT: E 497 LYS cc_start: 0.6995 (mptt) cc_final: 0.6771 (mptt) REVERT: a 3 GLU cc_start: 0.8158 (mp0) cc_final: 0.7954 (mp0) REVERT: a 23 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7087 (tp) REVERT: a 64 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7839 (mtt180) REVERT: a 77 GLU cc_start: 0.6637 (tp30) cc_final: 0.6323 (tp30) REVERT: a 128 GLN cc_start: 0.7331 (tm-30) cc_final: 0.7125 (tm-30) REVERT: a 132 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7990 (tp) REVERT: a 145 THR cc_start: 0.7461 (m) cc_final: 0.6973 (m) REVERT: a 196 GLU cc_start: 0.6974 (pm20) cc_final: 0.6621 (pm20) REVERT: a 304 LYS cc_start: 0.8066 (mttt) cc_final: 0.7764 (mttt) REVERT: a 392 ASP cc_start: 0.8020 (m-30) cc_final: 0.7632 (m-30) REVERT: a 431 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6974 (p0) REVERT: b 27 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6862 (mt-10) outliers start: 75 outliers final: 24 residues processed: 672 average time/residue: 0.6508 time to fit residues: 489.7147 Evaluate side-chains 596 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 564 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1177 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 431 ASP Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 94 optimal weight: 0.5980 chunk 80 optimal weight: 0.2980 chunk 227 optimal weight: 0.7980 chunk 224 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 244 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 HIS D 77 HIS ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 ASN D 515 GLN D 541 ASN D 619 HIS D 661 GLN D1049 HIS G 57 HIS G 63 ASN G 155 GLN E 123 GLN a 50 ASN a 101 ASN ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 216 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 256 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135827 restraints weight = 27624.426| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.72 r_work: 0.3654 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21516 Z= 0.110 Angle : 0.475 6.399 29182 Z= 0.237 Chirality : 0.040 0.136 3301 Planarity : 0.004 0.041 3757 Dihedral : 9.822 170.723 2936 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.35 % Allowed : 16.07 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: -0.18 (0.16), residues: 2654 helix: 0.94 (0.15), residues: 1343 sheet: -0.90 (0.30), residues: 246 loop : -1.25 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 665 TYR 0.012 0.001 TYR a 272 PHE 0.024 0.001 PHE b 367 TRP 0.010 0.001 TRP b 21 HIS 0.007 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00263 (21516) covalent geometry : angle 0.47483 (29182) hydrogen bonds : bond 0.03491 ( 936) hydrogen bonds : angle 3.57609 ( 2748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 575 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.6607 (t0) cc_final: 0.6106 (t0) REVERT: D 360 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7561 (mmm160) REVERT: D 398 ASP cc_start: 0.7541 (m-30) cc_final: 0.7279 (m-30) REVERT: D 452 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6524 (mm-30) REVERT: D 596 GLU cc_start: 0.7161 (tt0) cc_final: 0.6933 (tt0) REVERT: D 641 ARG cc_start: 0.8383 (mmp-170) cc_final: 0.8096 (mmp80) REVERT: D 725 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7860 (mmt) REVERT: D 743 LYS cc_start: 0.7408 (tttt) cc_final: 0.7142 (mmtt) REVERT: D 859 TYR cc_start: 0.8289 (m-80) cc_final: 0.8079 (m-80) REVERT: D 903 MET cc_start: 0.8319 (tpt) cc_final: 0.8082 (mmm) REVERT: D 1111 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8201 (tp) REVERT: G 10 MET cc_start: 0.7952 (ttm) cc_final: 0.7717 (mtt) REVERT: G 15 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7425 (ttm110) REVERT: G 140 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7703 (mt-10) REVERT: G 175 ASP cc_start: 0.7830 (t70) cc_final: 0.7612 (t0) REVERT: E 122 GLN cc_start: 0.6665 (mm-40) cc_final: 0.6356 (mm-40) REVERT: E 213 GLN cc_start: 0.8066 (mt0) cc_final: 0.7865 (mt0) REVERT: E 321 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7232 (mm-40) REVERT: E 327 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7148 (mm-30) REVERT: E 379 ARG cc_start: 0.6469 (ttt90) cc_final: 0.6005 (ttt90) REVERT: E 387 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8061 (ttpp) REVERT: E 446 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6940 (mt) REVERT: a 3 GLU cc_start: 0.8163 (mp0) cc_final: 0.7369 (mt-10) REVERT: a 66 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8276 (p) REVERT: a 77 GLU cc_start: 0.6721 (tp30) cc_final: 0.6398 (tp30) REVERT: a 128 GLN cc_start: 0.7320 (tm-30) cc_final: 0.7070 (tm-30) REVERT: a 196 GLU cc_start: 0.7136 (pm20) cc_final: 0.6741 (pm20) REVERT: a 202 PHE cc_start: 0.8291 (m-80) cc_final: 0.7884 (m-80) REVERT: a 207 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6830 (mt-10) REVERT: a 251 ASP cc_start: 0.6884 (m-30) cc_final: 0.6619 (p0) REVERT: a 304 LYS cc_start: 0.8122 (mttt) cc_final: 0.7839 (mttt) REVERT: a 320 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8150 (mtp85) REVERT: b 180 VAL cc_start: 0.8554 (p) cc_final: 0.8324 (m) outliers start: 77 outliers final: 30 residues processed: 600 average time/residue: 0.7176 time to fit residues: 479.0608 Evaluate side-chains 595 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 559 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 113 GLU Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 305 CYS Chi-restraints excluded: chain a residue 315 CYS Chi-restraints excluded: chain a residue 332 ILE Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 chunk 181 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 515 GLN D 541 ASN D 661 GLN ** D 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1086 GLN G 125 ASN G 155 GLN E 130 GLN E 472 GLN ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 216 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.132979 restraints weight = 27513.117| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.71 r_work: 0.3611 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21516 Z= 0.117 Angle : 0.486 7.845 29182 Z= 0.241 Chirality : 0.040 0.135 3301 Planarity : 0.004 0.039 3757 Dihedral : 9.830 177.869 2934 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.48 % Allowed : 16.68 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 (0.16), residues: 2654 helix: 1.21 (0.15), residues: 1356 sheet: -0.61 (0.31), residues: 246 loop : -1.02 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 665 TYR 0.012 0.001 TYR D 107 PHE 0.021 0.001 PHE b 367 TRP 0.010 0.001 TRP b 21 HIS 0.006 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00279 (21516) covalent geometry : angle 0.48587 (29182) hydrogen bonds : bond 0.03435 ( 936) hydrogen bonds : angle 3.50251 ( 2748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 567 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7100 (t0) cc_final: 0.6641 (t0) REVERT: D 398 ASP cc_start: 0.7474 (m-30) cc_final: 0.7209 (m-30) REVERT: D 452 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6586 (mm-30) REVERT: D 563 MET cc_start: 0.8319 (mtp) cc_final: 0.8090 (mtp) REVERT: D 596 GLU cc_start: 0.7151 (tt0) cc_final: 0.6931 (tt0) REVERT: D 725 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8072 (tpp) REVERT: D 743 LYS cc_start: 0.7507 (tttt) cc_final: 0.7242 (mmtt) REVERT: D 765 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7931 (mtt90) REVERT: D 876 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7042 (mtp) REVERT: D 903 MET cc_start: 0.8295 (tpt) cc_final: 0.8005 (mmm) REVERT: D 1111 LEU cc_start: 0.8453 (tp) cc_final: 0.8217 (tp) REVERT: D 1139 TYR cc_start: 0.8519 (m-80) cc_final: 0.8277 (m-80) REVERT: G 15 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7332 (ttm110) REVERT: G 92 ASP cc_start: 0.7109 (t70) cc_final: 0.6761 (t0) REVERT: G 140 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7695 (mt-10) REVERT: G 175 ASP cc_start: 0.7794 (t70) cc_final: 0.7571 (t0) REVERT: E 122 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6371 (mm-40) REVERT: E 162 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7765 (tttm) REVERT: E 213 GLN cc_start: 0.8100 (mt0) cc_final: 0.7892 (mt0) REVERT: E 246 ARG cc_start: 0.7362 (ptm160) cc_final: 0.7069 (ptm160) REVERT: E 321 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7212 (mm-40) REVERT: E 327 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7177 (mm-30) REVERT: E 379 ARG cc_start: 0.6462 (ttt90) cc_final: 0.5955 (ttt90) REVERT: E 387 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8083 (ttpp) REVERT: E 446 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7148 (mt) REVERT: a 3 GLU cc_start: 0.8149 (mp0) cc_final: 0.7491 (mp0) REVERT: a 66 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8320 (p) REVERT: a 112 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7750 (ttpp) REVERT: a 128 GLN cc_start: 0.7310 (tm-30) cc_final: 0.7025 (tm-30) REVERT: a 196 GLU cc_start: 0.7196 (pm20) cc_final: 0.6813 (pm20) REVERT: a 207 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6807 (mt-10) REVERT: a 304 LYS cc_start: 0.8191 (mttt) cc_final: 0.7743 (mttt) REVERT: a 320 ARG cc_start: 0.8374 (mtp180) cc_final: 0.8173 (ttm-80) REVERT: a 411 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6477 (mm-30) REVERT: b 27 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7639 (mt-10) REVERT: b 86 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7267 (mtp85) REVERT: b 180 VAL cc_start: 0.8673 (p) cc_final: 0.8381 (m) REVERT: b 333 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7246 (m) REVERT: b 401 GLU cc_start: 0.7502 (tp30) cc_final: 0.7246 (mp0) outliers start: 80 outliers final: 36 residues processed: 600 average time/residue: 0.7673 time to fit residues: 512.0012 Evaluate side-chains 585 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 541 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 315 CYS Chi-restraints excluded: chain a residue 332 ILE Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 433 GLU Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 81 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 219 optimal weight: 0.0870 chunk 187 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 144 HIS D 541 ASN D 661 GLN ** D 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN D1086 GLN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130750 restraints weight = 27325.026| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.69 r_work: 0.3579 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21516 Z= 0.141 Angle : 0.505 8.726 29182 Z= 0.249 Chirality : 0.041 0.152 3301 Planarity : 0.004 0.043 3757 Dihedral : 9.932 179.575 2934 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.22 % Allowed : 17.86 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.39 (0.16), residues: 2654 helix: 1.30 (0.14), residues: 1352 sheet: -0.42 (0.31), residues: 246 loop : -0.91 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1120 TYR 0.013 0.001 TYR D 107 PHE 0.020 0.002 PHE b 367 TRP 0.011 0.001 TRP E 527 HIS 0.007 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00351 (21516) covalent geometry : angle 0.50514 (29182) hydrogen bonds : bond 0.03762 ( 936) hydrogen bonds : angle 3.56244 ( 2748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 558 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7347 (t0) cc_final: 0.6859 (t0) REVERT: D 134 ASP cc_start: 0.7603 (m-30) cc_final: 0.7388 (m-30) REVERT: D 220 VAL cc_start: 0.7349 (OUTLIER) cc_final: 0.7043 (m) REVERT: D 225 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.6786 (ttp) REVERT: D 398 ASP cc_start: 0.7534 (m-30) cc_final: 0.7271 (m-30) REVERT: D 452 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6582 (mm-30) REVERT: D 563 MET cc_start: 0.8426 (mtp) cc_final: 0.8139 (mtp) REVERT: D 596 GLU cc_start: 0.7109 (tt0) cc_final: 0.6908 (tt0) REVERT: D 641 ARG cc_start: 0.8376 (mmp-170) cc_final: 0.8150 (mmp-170) REVERT: D 743 LYS cc_start: 0.7526 (tttt) cc_final: 0.7315 (mttt) REVERT: D 903 MET cc_start: 0.8268 (tpt) cc_final: 0.7969 (mmm) REVERT: D 979 ARG cc_start: 0.8023 (tmm-80) cc_final: 0.7631 (ttm170) REVERT: D 1111 LEU cc_start: 0.8474 (tp) cc_final: 0.8242 (tp) REVERT: G 15 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7282 (ttm110) REVERT: G 92 ASP cc_start: 0.7135 (t70) cc_final: 0.6788 (t0) REVERT: G 140 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7678 (mt-10) REVERT: G 175 ASP cc_start: 0.7813 (t70) cc_final: 0.7586 (t0) REVERT: E 122 GLN cc_start: 0.6678 (mm-40) cc_final: 0.6366 (mm-40) REVERT: E 162 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7811 (tttm) REVERT: E 246 ARG cc_start: 0.7434 (ptm160) cc_final: 0.7127 (ptm160) REVERT: E 321 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7154 (mm-40) REVERT: E 327 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7204 (mm-30) REVERT: E 379 ARG cc_start: 0.6471 (ttt90) cc_final: 0.5967 (ttt90) REVERT: E 387 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8100 (ttpp) REVERT: E 446 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7225 (mt) REVERT: E 469 MET cc_start: 0.8122 (ttt) cc_final: 0.7616 (ttt) REVERT: E 490 LEU cc_start: 0.8385 (mm) cc_final: 0.8113 (mp) REVERT: a 3 GLU cc_start: 0.8228 (mp0) cc_final: 0.7250 (mt-10) REVERT: a 66 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8278 (p) REVERT: a 112 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7742 (ttpp) REVERT: a 128 GLN cc_start: 0.7303 (tm-30) cc_final: 0.7016 (tm-30) REVERT: a 196 GLU cc_start: 0.7264 (pm20) cc_final: 0.6912 (pm20) REVERT: a 300 ASN cc_start: 0.8118 (m-40) cc_final: 0.7911 (m-40) REVERT: a 313 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7994 (mtp) REVERT: a 411 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6496 (mm-30) REVERT: a 429 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7458 (tt0) REVERT: b 27 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7703 (mt-10) REVERT: b 86 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7268 (mtp85) REVERT: b 180 VAL cc_start: 0.8675 (p) cc_final: 0.8429 (m) REVERT: b 333 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7236 (m) REVERT: b 376 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8354 (mm-30) outliers start: 74 outliers final: 39 residues processed: 589 average time/residue: 0.7159 time to fit residues: 469.0294 Evaluate side-chains 590 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 542 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 313 MET Chi-restraints excluded: chain a residue 332 ILE Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 401 LYS Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 244 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 76 optimal weight: 0.0040 chunk 69 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 541 ASN D 661 GLN ** D 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN D1013 GLN D1049 HIS D1086 GLN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN E 136 ASN E 154 ASN E 262 ASN a 11 GLN a 15 GLN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129618 restraints weight = 27251.431| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.96 r_work: 0.3565 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21516 Z= 0.116 Angle : 0.477 8.716 29182 Z= 0.235 Chirality : 0.040 0.139 3301 Planarity : 0.004 0.045 3757 Dihedral : 9.884 179.820 2934 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.40 % Allowed : 17.99 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.59 (0.16), residues: 2654 helix: 1.44 (0.14), residues: 1361 sheet: -0.31 (0.31), residues: 246 loop : -0.80 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 79 TYR 0.014 0.001 TYR b 425 PHE 0.018 0.001 PHE b 367 TRP 0.010 0.001 TRP E 527 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00285 (21516) covalent geometry : angle 0.47676 (29182) hydrogen bonds : bond 0.03453 ( 936) hydrogen bonds : angle 3.50459 ( 2748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 558 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7345 (t0) cc_final: 0.6849 (t0) REVERT: D 134 ASP cc_start: 0.7637 (m-30) cc_final: 0.7383 (m-30) REVERT: D 220 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7020 (m) REVERT: D 225 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.6876 (ttp) REVERT: D 398 ASP cc_start: 0.7588 (m-30) cc_final: 0.7310 (m-30) REVERT: D 405 ASP cc_start: 0.7634 (t70) cc_final: 0.7377 (t0) REVERT: D 452 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6624 (mm-30) REVERT: D 563 MET cc_start: 0.8465 (mtp) cc_final: 0.8172 (mtp) REVERT: D 596 GLU cc_start: 0.7165 (tt0) cc_final: 0.6943 (tt0) REVERT: D 743 LYS cc_start: 0.7559 (tttt) cc_final: 0.7341 (mttt) REVERT: D 840 VAL cc_start: 0.8382 (p) cc_final: 0.8150 (m) REVERT: D 903 MET cc_start: 0.8284 (tpt) cc_final: 0.8002 (mmm) REVERT: D 979 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7682 (ttm110) REVERT: D 1111 LEU cc_start: 0.8491 (tp) cc_final: 0.8246 (tp) REVERT: G 15 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7256 (ttm110) REVERT: G 73 LEU cc_start: 0.7536 (mp) cc_final: 0.7297 (mt) REVERT: G 92 ASP cc_start: 0.7198 (t70) cc_final: 0.6872 (t0) REVERT: G 140 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7737 (mt-10) REVERT: G 175 ASP cc_start: 0.7851 (t70) cc_final: 0.7603 (t0) REVERT: E 122 GLN cc_start: 0.6708 (mm-40) cc_final: 0.6305 (mm-40) REVERT: E 213 GLN cc_start: 0.8232 (mt0) cc_final: 0.8017 (mt0) REVERT: E 246 ARG cc_start: 0.7542 (ptm160) cc_final: 0.7208 (ptm160) REVERT: E 321 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: E 327 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 387 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: E 442 LYS cc_start: 0.8231 (mtmm) cc_final: 0.8029 (mtmm) REVERT: E 446 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7227 (mt) REVERT: E 469 MET cc_start: 0.8148 (ttt) cc_final: 0.7724 (ttt) REVERT: E 490 LEU cc_start: 0.8401 (mm) cc_final: 0.8138 (mp) REVERT: a 3 GLU cc_start: 0.8164 (mp0) cc_final: 0.7570 (mp0) REVERT: a 66 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8332 (p) REVERT: a 112 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7775 (ttpp) REVERT: a 128 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7067 (tm-30) REVERT: a 196 GLU cc_start: 0.7339 (pm20) cc_final: 0.6958 (pm20) REVERT: a 221 ARG cc_start: 0.6994 (mtm110) cc_final: 0.6754 (mtm110) REVERT: a 300 ASN cc_start: 0.8173 (m-40) cc_final: 0.7927 (m-40) REVERT: a 304 LYS cc_start: 0.8248 (mttt) cc_final: 0.7964 (mttt) REVERT: a 313 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: a 411 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6579 (mm-30) REVERT: b 86 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7328 (mtp85) REVERT: b 180 VAL cc_start: 0.8696 (p) cc_final: 0.8454 (m) REVERT: b 333 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7202 (m) REVERT: b 401 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7414 (mp0) outliers start: 78 outliers final: 46 residues processed: 588 average time/residue: 0.7040 time to fit residues: 459.1324 Evaluate side-chains 597 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 541 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 979 ARG Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 386 ARG Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 214 ARG Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 313 MET Chi-restraints excluded: chain a residue 332 ILE Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 401 LYS Chi-restraints excluded: chain a residue 433 GLU Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 395 LEU Chi-restraints excluded: chain b residue 401 GLU Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 199 optimal weight: 1.9990 chunk 139 optimal weight: 0.0170 chunk 262 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 122 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 541 ASN D 661 GLN D 827 GLN D1013 GLN D1049 HIS D1086 GLN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 HIS E 240 ASN E 262 ASN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 GLN b 195 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131307 restraints weight = 26808.314| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.79 r_work: 0.3586 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21516 Z= 0.106 Angle : 0.465 9.025 29182 Z= 0.230 Chirality : 0.039 0.125 3301 Planarity : 0.004 0.047 3757 Dihedral : 9.811 178.581 2934 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.27 % Allowed : 18.64 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.75 (0.16), residues: 2654 helix: 1.56 (0.14), residues: 1360 sheet: -0.21 (0.31), residues: 246 loop : -0.72 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 79 TYR 0.017 0.001 TYR D1139 PHE 0.017 0.001 PHE b 367 TRP 0.008 0.001 TRP E 527 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00257 (21516) covalent geometry : angle 0.46526 (29182) hydrogen bonds : bond 0.03317 ( 936) hydrogen bonds : angle 3.44165 ( 2748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 550 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7336 (t0) cc_final: 0.6892 (t0) REVERT: D 134 ASP cc_start: 0.7568 (m-30) cc_final: 0.7294 (m-30) REVERT: D 220 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7036 (m) REVERT: D 225 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.6827 (ttp) REVERT: D 398 ASP cc_start: 0.7477 (m-30) cc_final: 0.7185 (m-30) REVERT: D 405 ASP cc_start: 0.7656 (t70) cc_final: 0.7394 (t0) REVERT: D 452 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6664 (mm-30) REVERT: D 563 MET cc_start: 0.8452 (mtp) cc_final: 0.8238 (mtm) REVERT: D 596 GLU cc_start: 0.7194 (tt0) cc_final: 0.6961 (tt0) REVERT: D 743 LYS cc_start: 0.7559 (tttt) cc_final: 0.7340 (mttt) REVERT: D 840 VAL cc_start: 0.8396 (p) cc_final: 0.8144 (m) REVERT: D 903 MET cc_start: 0.8283 (tpt) cc_final: 0.7989 (mmm) REVERT: D 979 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7690 (ttm110) REVERT: D 1111 LEU cc_start: 0.8478 (tp) cc_final: 0.8214 (tp) REVERT: G 15 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7212 (ttm110) REVERT: G 73 LEU cc_start: 0.7514 (mp) cc_final: 0.7271 (mt) REVERT: G 92 ASP cc_start: 0.7126 (t70) cc_final: 0.6833 (t0) REVERT: G 140 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7666 (mt-10) REVERT: G 175 ASP cc_start: 0.7818 (t70) cc_final: 0.7485 (t0) REVERT: E 122 GLN cc_start: 0.6618 (mm-40) cc_final: 0.6268 (mm-40) REVERT: E 125 GLN cc_start: 0.7285 (mt0) cc_final: 0.7049 (mp10) REVERT: E 246 ARG cc_start: 0.7477 (ptm160) cc_final: 0.7161 (ptm160) REVERT: E 321 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7240 (mm-40) REVERT: E 327 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7226 (mm-30) REVERT: E 387 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8123 (ttpp) REVERT: E 446 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7182 (mt) REVERT: E 469 MET cc_start: 0.8140 (ttt) cc_final: 0.7756 (ttt) REVERT: E 490 LEU cc_start: 0.8406 (mm) cc_final: 0.8151 (mp) REVERT: a 3 GLU cc_start: 0.8192 (mp0) cc_final: 0.7411 (mt-10) REVERT: a 112 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7723 (ttpp) REVERT: a 128 GLN cc_start: 0.7382 (tm-30) cc_final: 0.7074 (tm-30) REVERT: a 196 GLU cc_start: 0.7312 (pm20) cc_final: 0.6964 (pm20) REVERT: a 221 ARG cc_start: 0.6926 (mtm110) cc_final: 0.6662 (mtm110) REVERT: a 300 ASN cc_start: 0.8200 (m-40) cc_final: 0.7944 (m-40) REVERT: a 304 LYS cc_start: 0.8272 (mttt) cc_final: 0.7990 (mttt) REVERT: a 313 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7866 (mtp) REVERT: a 411 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6516 (mm-30) REVERT: b 27 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7672 (mt-10) REVERT: b 86 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7334 (mtp85) REVERT: b 180 VAL cc_start: 0.8709 (p) cc_final: 0.8476 (m) REVERT: b 333 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7197 (m) REVERT: b 401 GLU cc_start: 0.7602 (tp30) cc_final: 0.7390 (mp0) outliers start: 75 outliers final: 46 residues processed: 582 average time/residue: 0.7740 time to fit residues: 500.0612 Evaluate side-chains 590 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 536 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 802 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 979 ARG Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1136 LEU Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 214 ARG Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 313 MET Chi-restraints excluded: chain a residue 315 CYS Chi-restraints excluded: chain a residue 332 ILE Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 401 LYS Chi-restraints excluded: chain a residue 433 GLU Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 231 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 209 optimal weight: 0.3980 chunk 164 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 541 ASN D 661 GLN D 827 GLN D1013 GLN D1049 HIS D1086 GLN G 51 ASN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 262 ASN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130399 restraints weight = 26720.548| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.80 r_work: 0.3573 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21516 Z= 0.125 Angle : 0.489 9.104 29182 Z= 0.241 Chirality : 0.040 0.124 3301 Planarity : 0.004 0.049 3757 Dihedral : 9.832 179.271 2934 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.05 % Allowed : 19.25 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.80 (0.16), residues: 2654 helix: 1.58 (0.14), residues: 1365 sheet: -0.07 (0.32), residues: 243 loop : -0.69 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 585 TYR 0.018 0.001 TYR D1139 PHE 0.017 0.001 PHE b 367 TRP 0.009 0.001 TRP E 527 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00310 (21516) covalent geometry : angle 0.48939 (29182) hydrogen bonds : bond 0.03543 ( 936) hydrogen bonds : angle 3.49578 ( 2748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 546 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7402 (t0) cc_final: 0.6983 (t0) REVERT: D 134 ASP cc_start: 0.7618 (m-30) cc_final: 0.7333 (m-30) REVERT: D 225 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.6872 (ttp) REVERT: D 398 ASP cc_start: 0.7518 (m-30) cc_final: 0.7232 (m-30) REVERT: D 405 ASP cc_start: 0.7660 (t70) cc_final: 0.7393 (t0) REVERT: D 452 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6669 (mm-30) REVERT: D 563 MET cc_start: 0.8472 (mtp) cc_final: 0.8246 (mtm) REVERT: D 596 GLU cc_start: 0.7200 (tt0) cc_final: 0.6971 (tt0) REVERT: D 678 GLN cc_start: 0.8187 (tp40) cc_final: 0.7960 (tp40) REVERT: D 695 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7669 (ttm-80) REVERT: D 743 LYS cc_start: 0.7612 (tttt) cc_final: 0.7400 (mttt) REVERT: D 840 VAL cc_start: 0.8421 (p) cc_final: 0.8165 (m) REVERT: D 903 MET cc_start: 0.8299 (tpt) cc_final: 0.8001 (mmm) REVERT: D 979 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7704 (ttm110) REVERT: D 1111 LEU cc_start: 0.8488 (tp) cc_final: 0.8226 (tp) REVERT: G 15 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7225 (ttm110) REVERT: G 73 LEU cc_start: 0.7514 (mp) cc_final: 0.7264 (mt) REVERT: G 92 ASP cc_start: 0.7169 (t70) cc_final: 0.6847 (t0) REVERT: G 140 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7688 (mt-10) REVERT: G 175 ASP cc_start: 0.7820 (t70) cc_final: 0.7571 (t0) REVERT: E 122 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6293 (mm-40) REVERT: E 246 ARG cc_start: 0.7470 (ptm160) cc_final: 0.7157 (ptm160) REVERT: E 321 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7257 (mm-40) REVERT: E 327 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7221 (mm-30) REVERT: E 387 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8125 (ttpp) REVERT: E 446 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7208 (mt) REVERT: E 490 LEU cc_start: 0.8403 (mm) cc_final: 0.8152 (mp) REVERT: a 3 GLU cc_start: 0.8191 (mp0) cc_final: 0.7442 (mt-10) REVERT: a 27 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7438 (mt-10) REVERT: a 112 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7731 (ttpp) REVERT: a 128 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7052 (tm-30) REVERT: a 136 LEU cc_start: 0.8461 (mt) cc_final: 0.8252 (mp) REVERT: a 196 GLU cc_start: 0.7282 (pm20) cc_final: 0.6934 (pm20) REVERT: a 221 ARG cc_start: 0.6968 (mtm110) cc_final: 0.6694 (mtm110) REVERT: a 300 ASN cc_start: 0.8244 (m-40) cc_final: 0.7968 (m-40) REVERT: a 304 LYS cc_start: 0.8290 (mttt) cc_final: 0.8014 (mttt) REVERT: a 313 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7903 (mtp) REVERT: a 320 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8265 (mtm180) REVERT: a 411 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6502 (mm-30) REVERT: b 27 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7664 (mt-10) REVERT: b 86 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7334 (mtp85) REVERT: b 180 VAL cc_start: 0.8708 (p) cc_final: 0.8492 (m) REVERT: b 333 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7150 (m) REVERT: b 401 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7395 (mp0) outliers start: 70 outliers final: 49 residues processed: 575 average time/residue: 0.7301 time to fit residues: 466.0555 Evaluate side-chains 596 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 540 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 802 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1085 ILE Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1136 LEU Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 113 GLU Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 207 GLU Chi-restraints excluded: chain a residue 214 ARG Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 313 MET Chi-restraints excluded: chain a residue 315 CYS Chi-restraints excluded: chain a residue 332 ILE Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 401 LYS Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 401 GLU Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 34 optimal weight: 0.5980 chunk 185 optimal weight: 0.8980 chunk 251 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.0070 chunk 68 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 253 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 541 ASN D 661 GLN D 827 GLN D1013 GLN D1049 HIS D1086 GLN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 262 ASN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 GLN ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130665 restraints weight = 26777.169| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.87 r_work: 0.3573 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21516 Z= 0.108 Angle : 0.481 10.780 29182 Z= 0.236 Chirality : 0.040 0.122 3301 Planarity : 0.004 0.050 3757 Dihedral : 9.801 178.827 2934 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.79 % Allowed : 19.90 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.92 (0.16), residues: 2654 helix: 1.67 (0.14), residues: 1365 sheet: -0.00 (0.32), residues: 243 loop : -0.62 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 585 TYR 0.020 0.001 TYR D1139 PHE 0.016 0.001 PHE b 367 TRP 0.008 0.001 TRP b 344 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00262 (21516) covalent geometry : angle 0.48074 (29182) hydrogen bonds : bond 0.03330 ( 936) hydrogen bonds : angle 3.45166 ( 2748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 548 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7560 (t0) cc_final: 0.7095 (t0) REVERT: D 134 ASP cc_start: 0.7617 (m-30) cc_final: 0.7343 (m-30) REVERT: D 225 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.6866 (ttp) REVERT: D 398 ASP cc_start: 0.7529 (m-30) cc_final: 0.7241 (m-30) REVERT: D 405 ASP cc_start: 0.7663 (t70) cc_final: 0.7406 (t0) REVERT: D 452 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6673 (mm-30) REVERT: D 563 MET cc_start: 0.8456 (mtp) cc_final: 0.8235 (mtm) REVERT: D 743 LYS cc_start: 0.7630 (tttt) cc_final: 0.7409 (mttt) REVERT: D 765 ARG cc_start: 0.8313 (mtt90) cc_final: 0.8091 (mtt90) REVERT: D 840 VAL cc_start: 0.8415 (p) cc_final: 0.8159 (m) REVERT: D 903 MET cc_start: 0.8303 (tpt) cc_final: 0.8003 (mmm) REVERT: D 979 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7633 (ttm110) REVERT: D 1111 LEU cc_start: 0.8484 (tp) cc_final: 0.8217 (tp) REVERT: G 15 ARG cc_start: 0.7477 (ttm110) cc_final: 0.7192 (ttm110) REVERT: G 73 LEU cc_start: 0.7510 (mp) cc_final: 0.7261 (mt) REVERT: G 140 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7660 (mt-10) REVERT: G 175 ASP cc_start: 0.7817 (t70) cc_final: 0.7554 (t0) REVERT: E 122 GLN cc_start: 0.6665 (mm-40) cc_final: 0.6317 (mm-40) REVERT: E 246 ARG cc_start: 0.7493 (ptm160) cc_final: 0.7173 (ptm160) REVERT: E 327 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7242 (mm-30) REVERT: E 387 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8138 (ttpp) REVERT: E 446 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7186 (mt) REVERT: E 490 LEU cc_start: 0.8424 (mm) cc_final: 0.8169 (mp) REVERT: a 3 GLU cc_start: 0.8148 (mp0) cc_final: 0.7466 (mt-10) REVERT: a 112 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7711 (ttpp) REVERT: a 128 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7078 (tm-30) REVERT: a 136 LEU cc_start: 0.8433 (mt) cc_final: 0.8220 (mp) REVERT: a 196 GLU cc_start: 0.7299 (pm20) cc_final: 0.6939 (pm20) REVERT: a 300 ASN cc_start: 0.8262 (m-40) cc_final: 0.7980 (m-40) REVERT: a 304 LYS cc_start: 0.8302 (mttt) cc_final: 0.8024 (mttt) REVERT: a 313 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: a 320 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8266 (mtm180) REVERT: a 411 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6523 (mm-30) REVERT: b 27 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7669 (mt-10) REVERT: b 86 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7334 (mtp85) REVERT: b 180 VAL cc_start: 0.8704 (p) cc_final: 0.8489 (m) REVERT: b 333 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7083 (m) REVERT: b 359 ARG cc_start: 0.7292 (ttt90) cc_final: 0.7082 (ttt90) REVERT: b 401 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7414 (mp0) outliers start: 64 outliers final: 47 residues processed: 572 average time/residue: 0.7557 time to fit residues: 479.1941 Evaluate side-chains 596 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 543 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 802 THR Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1136 LEU Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 113 GLU Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 207 GLU Chi-restraints excluded: chain a residue 214 ARG Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 250 VAL Chi-restraints excluded: chain a residue 313 MET Chi-restraints excluded: chain a residue 315 CYS Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain a residue 433 GLU Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 401 GLU Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 169 optimal weight: 0.0030 chunk 227 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 0.0060 chunk 211 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 541 ASN D 661 GLN D 827 GLN D1013 GLN D1049 HIS D1086 GLN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 262 ASN E 281 GLN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 133 GLN b 83 GLN b 195 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130091 restraints weight = 26813.222| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.88 r_work: 0.3564 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21516 Z= 0.120 Angle : 0.497 10.911 29182 Z= 0.243 Chirality : 0.040 0.124 3301 Planarity : 0.004 0.052 3757 Dihedral : 9.840 179.115 2934 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 20.03 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.95 (0.16), residues: 2654 helix: 1.67 (0.14), residues: 1364 sheet: 0.00 (0.32), residues: 243 loop : -0.58 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 585 TYR 0.021 0.001 TYR D1139 PHE 0.016 0.001 PHE b 367 TRP 0.008 0.001 TRP E 527 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00297 (21516) covalent geometry : angle 0.49726 (29182) hydrogen bonds : bond 0.03503 ( 936) hydrogen bonds : angle 3.48752 ( 2748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 549 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 91 ASP cc_start: 0.7644 (t0) cc_final: 0.7171 (t0) REVERT: D 134 ASP cc_start: 0.7616 (m-30) cc_final: 0.7343 (m-30) REVERT: D 225 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.6904 (ttp) REVERT: D 398 ASP cc_start: 0.7520 (m-30) cc_final: 0.7237 (m-30) REVERT: D 405 ASP cc_start: 0.7681 (t70) cc_final: 0.7417 (t0) REVERT: D 452 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6690 (mm-30) REVERT: D 474 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: D 743 LYS cc_start: 0.7648 (tttt) cc_final: 0.7419 (mttt) REVERT: D 765 ARG cc_start: 0.8301 (mtt90) cc_final: 0.8077 (mtt90) REVERT: D 903 MET cc_start: 0.8311 (tpt) cc_final: 0.7996 (mmm) REVERT: D 979 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7636 (ttm170) REVERT: D 1111 LEU cc_start: 0.8495 (tp) cc_final: 0.8241 (tp) REVERT: G 15 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7213 (ttm110) REVERT: G 140 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7707 (mt-10) REVERT: G 175 ASP cc_start: 0.7834 (t70) cc_final: 0.7511 (t0) REVERT: E 122 GLN cc_start: 0.6680 (mm-40) cc_final: 0.6329 (mm-40) REVERT: E 246 ARG cc_start: 0.7492 (ptm160) cc_final: 0.7125 (ptm160) REVERT: E 321 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7172 (mm110) REVERT: E 327 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7257 (mm-30) REVERT: E 387 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (ttpp) REVERT: E 446 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7246 (mt) REVERT: E 469 MET cc_start: 0.8104 (ttt) cc_final: 0.7692 (ttt) REVERT: E 490 LEU cc_start: 0.8414 (mm) cc_final: 0.8164 (mp) REVERT: a 3 GLU cc_start: 0.8171 (mp0) cc_final: 0.7485 (mt-10) REVERT: a 64 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.8044 (mtt-85) REVERT: a 112 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7708 (ttpp) REVERT: a 128 GLN cc_start: 0.7382 (tm-30) cc_final: 0.7051 (tm-30) REVERT: a 136 LEU cc_start: 0.8462 (mt) cc_final: 0.8255 (mp) REVERT: a 196 GLU cc_start: 0.7301 (pm20) cc_final: 0.6943 (pm20) REVERT: a 300 ASN cc_start: 0.8292 (m-40) cc_final: 0.8000 (m-40) REVERT: a 304 LYS cc_start: 0.8331 (mttt) cc_final: 0.8055 (mttt) REVERT: a 313 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7923 (mtp) REVERT: a 411 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6520 (mm-30) REVERT: b 27 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7707 (mt-10) REVERT: b 86 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7333 (mtp85) REVERT: b 180 VAL cc_start: 0.8696 (p) cc_final: 0.8494 (m) REVERT: b 333 VAL cc_start: 0.7409 (OUTLIER) cc_final: 0.7080 (m) REVERT: b 401 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7444 (mp0) outliers start: 63 outliers final: 44 residues processed: 574 average time/residue: 0.7523 time to fit residues: 479.3494 Evaluate side-chains 591 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 539 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 191 GLN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 757 ILE Chi-restraints excluded: chain D residue 802 THR Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1086 GLN Chi-restraints excluded: chain D residue 1136 LEU Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 113 GLU Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 207 GLU Chi-restraints excluded: chain a residue 214 ARG Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 313 MET Chi-restraints excluded: chain a residue 315 CYS Chi-restraints excluded: chain a residue 381 THR Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 401 GLU Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 105 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 225 optimal weight: 0.2980 chunk 196 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 chunk 152 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 541 ASN ** D 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN D1013 GLN D1049 HIS D1086 GLN G 26 ASN G 125 ASN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 262 ASN ** a 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.130863 restraints weight = 26852.188| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.80 r_work: 0.3577 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21516 Z= 0.113 Angle : 0.495 10.914 29182 Z= 0.242 Chirality : 0.040 0.124 3301 Planarity : 0.004 0.051 3757 Dihedral : 9.834 178.962 2934 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.53 % Allowed : 20.47 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 1.02 (0.16), residues: 2654 helix: 1.73 (0.14), residues: 1361 sheet: 0.04 (0.32), residues: 243 loop : -0.54 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 585 TYR 0.022 0.001 TYR D1139 PHE 0.016 0.001 PHE b 367 TRP 0.008 0.001 TRP b 344 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00277 (21516) covalent geometry : angle 0.49460 (29182) hydrogen bonds : bond 0.03378 ( 936) hydrogen bonds : angle 3.46261 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11138.89 seconds wall clock time: 189 minutes 16.32 seconds (11356.32 seconds total)