Starting phenix.real_space_refine on Wed Mar 4 02:29:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y6k_10706/03_2026/6y6k_10706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y6k_10706/03_2026/6y6k_10706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y6k_10706/03_2026/6y6k_10706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y6k_10706/03_2026/6y6k_10706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y6k_10706/03_2026/6y6k_10706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y6k_10706/03_2026/6y6k_10706.map" } resolution = 3.78 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 63 5.16 5 C 6577 2.51 5 N 1786 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10351 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1299, 10350 Classifications: {'peptide': 1299} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1248} Chain breaks: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10351 At special positions: 0 Unit cell: (103.53, 98.31, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 Mg 1 11.99 O 1924 8.00 N 1786 7.00 C 6577 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: 0.81 Conformation dependent library (CDL) restraints added in 458.8 milliseconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 13 sheets defined 43.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 77 through 83 removed outlier: 3.662A pdb=" N ASP A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.503A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 removed outlier: 3.858A pdb=" N TYR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 184 through 207 removed outlier: 3.500A pdb=" N ALA A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.990A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.539A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 4.117A pdb=" N GLY A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.713A pdb=" N GLU A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 4.338A pdb=" N LYS A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.730A pdb=" N LEU A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.507A pdb=" N CYS A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.722A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 removed outlier: 4.216A pdb=" N LEU A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 removed outlier: 3.750A pdb=" N HIS A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A 504 " --> pdb=" O HIS A 500 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 removed outlier: 3.659A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 521 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 524 " --> pdb=" O TRP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 removed outlier: 3.662A pdb=" N THR A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 618 " --> pdb=" O CYS A 614 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 627 " --> pdb=" O TRP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 3.766A pdb=" N PHE A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 682 through 687 removed outlier: 4.111A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.504A pdb=" N ARG A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.530A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 4.402A pdb=" N GLU A 779 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 780 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A 781 " --> pdb=" O GLU A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 781' Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.674A pdb=" N LEU A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 4.248A pdb=" N GLU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 874 through 877 Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 893 through 902 removed outlier: 3.917A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 3.907A pdb=" N LEU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 940 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 961 removed outlier: 4.124A pdb=" N SER A 960 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.700A pdb=" N LYS A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.798A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 removed outlier: 3.501A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1056 removed outlier: 3.826A pdb=" N ASP A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.607A pdb=" N HIS A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1092 " --> pdb=" O SER A1088 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A1097 " --> pdb=" O CYS A1093 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1153 removed outlier: 3.633A pdb=" N PHE A1147 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A1148 " --> pdb=" O ARG A1144 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.543A pdb=" N ASN A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1195 through 1201 removed outlier: 3.515A pdb=" N ILE A1199 " --> pdb=" O THR A1195 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1200 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1195 through 1201' Processing helix chain 'A' and resid 1214 through 1219 Processing helix chain 'A' and resid 1222 through 1228 Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.754A pdb=" N LEU A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1248 removed outlier: 3.591A pdb=" N GLN A1242 " --> pdb=" O ILE A1238 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1244 " --> pdb=" O CYS A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1266 removed outlier: 3.790A pdb=" N LEU A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1296 removed outlier: 3.839A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1404 through 1411 removed outlier: 3.540A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.816A pdb=" N ARG A1462 " --> pdb=" O PRO A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1479 removed outlier: 3.612A pdb=" N VAL A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A1477 " --> pdb=" O ARG A1473 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A1479 " --> pdb=" O CYS A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.108A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 123 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS A 115 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 125 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 6.776A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.797A pdb=" N LYS A 544 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 912 Processing sheet with id=AA8, first strand: chain 'A' and resid 978 through 979 removed outlier: 3.510A pdb=" N ILE A1134 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 981 through 982 removed outlier: 5.798A pdb=" N ASN A 981 " --> pdb=" O ASN A1174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1024 through 1026 removed outlier: 3.896A pdb=" N THR A1074 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1179 through 1180 Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1487 removed outlier: 3.802A pdb=" N LYS A1487 " --> pdb=" O SER A1610 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A1610 " --> pdb=" O LYS A1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1496 through 1500 removed outlier: 3.835A pdb=" N SER A1498 " --> pdb=" O LEU A1583 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 741 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: 1.55 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2709 1.33 - 1.45: 1930 1.45 - 1.57: 5827 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 10568 Sorted by residual: bond pdb=" C MET A 181 " pdb=" N PRO A 182 " ideal model delta sigma weight residual 1.332 1.387 -0.056 1.32e-02 5.74e+03 1.78e+01 bond pdb=" N PRO A 182 " pdb=" CD PRO A 182 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB ASN A 981 " pdb=" CG ASN A 981 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.80e+00 bond pdb=" CA LEU A 214 " pdb=" C LEU A 214 " ideal model delta sigma weight residual 1.530 1.501 0.028 1.10e-02 8.26e+03 6.63e+00 bond pdb=" CB GLU A1123 " pdb=" CG GLU A1123 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.44e+00 ... (remaining 10563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 13950 2.72 - 5.44: 285 5.44 - 8.16: 31 8.16 - 10.88: 3 10.88 - 13.60: 3 Bond angle restraints: 14272 Sorted by residual: angle pdb=" N TYR A 861 " pdb=" CA TYR A 861 " pdb=" C TYR A 861 " ideal model delta sigma weight residual 111.36 123.61 -12.25 1.09e+00 8.42e-01 1.26e+02 angle pdb=" N ASN A 984 " pdb=" CA ASN A 984 " pdb=" C ASN A 984 " ideal model delta sigma weight residual 110.17 121.98 -11.81 1.51e+00 4.39e-01 6.12e+01 angle pdb=" N LEU A 957 " pdb=" CA LEU A 957 " pdb=" C LEU A 957 " ideal model delta sigma weight residual 111.28 119.08 -7.80 1.09e+00 8.42e-01 5.12e+01 angle pdb=" C MET A 181 " pdb=" N PRO A 182 " pdb=" CA PRO A 182 " ideal model delta sigma weight residual 119.76 113.93 5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" N ALA A 590 " pdb=" CA ALA A 590 " pdb=" C ALA A 590 " ideal model delta sigma weight residual 109.52 100.69 8.83 1.55e+00 4.16e-01 3.24e+01 ... (remaining 14267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5527 17.49 - 34.99: 662 34.99 - 52.48: 146 52.48 - 69.98: 29 69.98 - 87.47: 12 Dihedral angle restraints: 6376 sinusoidal: 2607 harmonic: 3769 Sorted by residual: dihedral pdb=" CA THR A 995 " pdb=" C THR A 995 " pdb=" N THR A 996 " pdb=" CA THR A 996 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLY A 688 " pdb=" C GLY A 688 " pdb=" N LYS A 689 " pdb=" CA LYS A 689 " ideal model delta harmonic sigma weight residual 180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER A 639 " pdb=" C SER A 639 " pdb=" N GLU A 640 " pdb=" CA GLU A 640 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1376 0.083 - 0.165: 183 0.165 - 0.248: 22 0.248 - 0.330: 3 0.330 - 0.413: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA TYR A 861 " pdb=" N TYR A 861 " pdb=" C TYR A 861 " pdb=" CB TYR A 861 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA ASN A 984 " pdb=" N ASN A 984 " pdb=" C ASN A 984 " pdb=" CB ASN A 984 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA MET A 208 " pdb=" N MET A 208 " pdb=" C MET A 208 " pdb=" CB MET A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1582 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 676 " 0.049 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO A 677 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 30 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 31 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1006 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO A1007 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1007 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1007 " -0.035 5.00e-02 4.00e+02 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.09: 7482 3.09 - 3.70: 13385 3.70 - 4.30: 19160 4.30 - 4.90: 33074 Nonbonded interactions: 73166 Sorted by model distance: nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 1.889 2.170 nonbonded pdb=" N ASN A 954 " pdb=" OD1 ASN A 954 " model vdw 2.159 3.120 nonbonded pdb=" OD1 ASN A 742 " pdb=" ND2 ASN A 745 " model vdw 2.240 3.120 nonbonded pdb=" N ASN A 990 " pdb=" OD1 ASN A 990 " model vdw 2.252 3.120 nonbonded pdb=" OD1 ASP A 209 " pdb=" N ASP A 211 " model vdw 2.256 3.120 ... (remaining 73161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.012 0.089 10568 Z= 0.502 Angle : 0.992 13.604 14272 Z= 0.588 Chirality : 0.060 0.413 1585 Planarity : 0.006 0.073 1821 Dihedral : 15.997 87.472 3936 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.47 % Favored : 87.37 % Rotamer: Outliers : 2.36 % Allowed : 20.30 % Favored : 77.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % 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: -5.70 (0.16), residues: 1283 helix: -4.20 (0.13), residues: 518 sheet: -2.02 (0.41), residues: 134 loop : -3.85 (0.18), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1295 TYR 0.022 0.003 TYR A1110 PHE 0.026 0.003 PHE A1010 TRP 0.021 0.003 TRP A 520 HIS 0.008 0.002 HIS A1246 Details of bonding type rmsd covalent geometry : bond 0.01170 (10568) covalent geometry : angle 0.99193 (14272) hydrogen bonds : bond 0.34222 ( 266) hydrogen bonds : angle 10.34311 ( 741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.396 Fit side-chains REVERT: A 563 HIS cc_start: 0.8693 (m90) cc_final: 0.8216 (m90) REVERT: A 597 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7978 (mp0) REVERT: A 636 LYS cc_start: 0.9053 (tttt) cc_final: 0.8678 (tttm) REVERT: A 710 MET cc_start: 0.9020 (mtp) cc_final: 0.8820 (mtm) REVERT: A 956 ARG cc_start: 0.7285 (ttp80) cc_final: 0.7071 (ptt90) REVERT: A 1123 GLU cc_start: 0.9146 (pp20) cc_final: 0.8925 (pp20) REVERT: A 1180 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: A 1261 PHE cc_start: 0.8677 (m-80) cc_final: 0.8434 (m-80) REVERT: A 1294 TRP cc_start: 0.8870 (t60) cc_final: 0.8283 (t60) outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 0.1073 time to fit residues: 21.8478 Evaluate side-chains 117 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 750 TRP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1255 HIS Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.0060 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 162 ASN A 185 GLN A 247 ASN A 500 HIS A 516 GLN A 618 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 853 ASN A 870 HIS A1203 HIS A1239 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110575 restraints weight = 14066.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108223 restraints weight = 18031.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108452 restraints weight = 21973.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.109205 restraints weight = 12146.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.110442 restraints weight = 9957.769| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10568 Z= 0.126 Angle : 0.613 8.259 14272 Z= 0.326 Chirality : 0.043 0.142 1585 Planarity : 0.005 0.063 1821 Dihedral : 7.419 65.452 1445 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 3.41 % Allowed : 21.00 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -4.69 (0.18), residues: 1283 helix: -3.25 (0.16), residues: 573 sheet: -0.81 (0.44), residues: 125 loop : -3.47 (0.20), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.012 0.001 TYR A1110 PHE 0.012 0.001 PHE A 911 TRP 0.014 0.001 TRP A 520 HIS 0.006 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00277 (10568) covalent geometry : angle 0.61251 (14272) hydrogen bonds : bond 0.05525 ( 266) hydrogen bonds : angle 5.58551 ( 741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.384 Fit side-chains REVERT: A 608 ASN cc_start: 0.8597 (t0) cc_final: 0.8232 (t0) REVERT: A 636 LYS cc_start: 0.8844 (tttt) cc_final: 0.8605 (tttm) REVERT: A 691 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8119 (p0) REVERT: A 754 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 863 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6476 (pp20) REVERT: A 1239 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: A 1278 MET cc_start: 0.8548 (tpp) cc_final: 0.8226 (mtt) REVERT: A 1290 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7842 (mmm160) outliers start: 39 outliers final: 18 residues processed: 145 average time/residue: 0.1058 time to fit residues: 21.4465 Evaluate side-chains 122 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 598 PHE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1239 GLN Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 59 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A1035 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111800 restraints weight = 14178.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.107209 restraints weight = 19820.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109207 restraints weight = 23765.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109583 restraints weight = 12886.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.110378 restraints weight = 11269.895| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10568 Z= 0.118 Angle : 0.562 8.262 14272 Z= 0.295 Chirality : 0.042 0.217 1585 Planarity : 0.004 0.054 1821 Dihedral : 6.621 58.973 1429 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 3.15 % Allowed : 22.48 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -4.07 (0.20), residues: 1283 helix: -2.64 (0.18), residues: 582 sheet: -0.40 (0.45), residues: 125 loop : -3.28 (0.20), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1582 TYR 0.012 0.001 TYR A 202 PHE 0.013 0.001 PHE A 911 TRP 0.012 0.001 TRP A 520 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00275 (10568) covalent geometry : angle 0.56214 (14272) hydrogen bonds : bond 0.04434 ( 266) hydrogen bonds : angle 4.92406 ( 741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.428 Fit side-chains REVERT: A 1 MET cc_start: 0.6149 (mmp) cc_final: 0.4266 (ptt) REVERT: A 608 ASN cc_start: 0.8678 (t0) cc_final: 0.8294 (t0) REVERT: A 691 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8103 (p0) REVERT: A 754 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7699 (t80) REVERT: A 863 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6419 (pp20) REVERT: A 1279 ASP cc_start: 0.8256 (m-30) cc_final: 0.7900 (m-30) REVERT: A 1294 TRP cc_start: 0.8821 (t60) cc_final: 0.8159 (t60) outliers start: 36 outliers final: 22 residues processed: 137 average time/residue: 0.0960 time to fit residues: 18.8649 Evaluate side-chains 124 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1203 HIS Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 247 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 821 HIS A 895 GLN A1239 GLN A1483 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.110823 restraints weight = 14290.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107086 restraints weight = 14934.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107288 restraints weight = 24268.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.108864 restraints weight = 12652.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.110656 restraints weight = 9291.371| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10568 Z= 0.164 Angle : 0.581 7.417 14272 Z= 0.306 Chirality : 0.043 0.140 1585 Planarity : 0.004 0.053 1821 Dihedral : 6.378 58.644 1427 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 3.50 % Allowed : 23.18 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -3.72 (0.20), residues: 1283 helix: -2.33 (0.19), residues: 577 sheet: -0.32 (0.44), residues: 127 loop : -3.11 (0.21), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1582 TYR 0.012 0.001 TYR A1110 PHE 0.015 0.001 PHE A 911 TRP 0.012 0.001 TRP A 520 HIS 0.004 0.001 HIS A1190 Details of bonding type rmsd covalent geometry : bond 0.00397 (10568) covalent geometry : angle 0.58149 (14272) hydrogen bonds : bond 0.04823 ( 266) hydrogen bonds : angle 4.88617 ( 741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.257 Fit side-chains REVERT: A 109 MET cc_start: 0.5895 (mtp) cc_final: 0.4892 (mtm) REVERT: A 608 ASN cc_start: 0.8658 (t0) cc_final: 0.8259 (t0) REVERT: A 641 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8644 (tp) REVERT: A 863 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6408 (pp20) REVERT: A 1294 TRP cc_start: 0.8855 (t60) cc_final: 0.8195 (t60) outliers start: 40 outliers final: 31 residues processed: 129 average time/residue: 0.0857 time to fit residues: 16.1094 Evaluate side-chains 126 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 0.0030 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 247 ASN A 644 GLN A 734 HIS A 799 HIS A 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112179 restraints weight = 14111.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109897 restraints weight = 20591.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110380 restraints weight = 25209.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111423 restraints weight = 13438.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112075 restraints weight = 10937.862| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10568 Z= 0.120 Angle : 0.541 6.235 14272 Z= 0.284 Chirality : 0.041 0.148 1585 Planarity : 0.004 0.051 1821 Dihedral : 6.122 55.946 1427 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 3.67 % Allowed : 22.57 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -3.43 (0.21), residues: 1283 helix: -2.05 (0.20), residues: 576 sheet: -0.12 (0.45), residues: 125 loop : -3.00 (0.21), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 956 TYR 0.010 0.001 TYR A1110 PHE 0.014 0.001 PHE A 911 TRP 0.012 0.001 TRP A 520 HIS 0.005 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00291 (10568) covalent geometry : angle 0.54056 (14272) hydrogen bonds : bond 0.04027 ( 266) hydrogen bonds : angle 4.62084 ( 741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.318 Fit side-chains REVERT: A 1 MET cc_start: 0.6351 (mmp) cc_final: 0.4573 (ptt) REVERT: A 26 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7585 (tp-100) REVERT: A 109 MET cc_start: 0.5265 (mtp) cc_final: 0.3756 (mtm) REVERT: A 221 LEU cc_start: 0.8281 (mt) cc_final: 0.7793 (mt) REVERT: A 247 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8327 (t0) REVERT: A 608 ASN cc_start: 0.8672 (t0) cc_final: 0.8259 (t0) REVERT: A 641 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 691 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8139 (p0) REVERT: A 863 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: A 1197 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8558 (ttp80) REVERT: A 1294 TRP cc_start: 0.8786 (t60) cc_final: 0.8169 (t60) outliers start: 42 outliers final: 32 residues processed: 137 average time/residue: 0.1011 time to fit residues: 19.7602 Evaluate side-chains 138 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1203 HIS Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 11 optimal weight: 30.0000 chunk 117 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110812 restraints weight = 14302.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.108660 restraints weight = 21075.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109514 restraints weight = 24224.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110046 restraints weight = 14132.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110657 restraints weight = 11714.907| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10568 Z= 0.149 Angle : 0.554 6.259 14272 Z= 0.291 Chirality : 0.042 0.136 1585 Planarity : 0.004 0.051 1821 Dihedral : 5.993 55.560 1425 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.94 % Allowed : 22.66 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -3.30 (0.21), residues: 1283 helix: -1.91 (0.20), residues: 576 sheet: -0.09 (0.45), residues: 125 loop : -2.96 (0.21), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 956 TYR 0.011 0.001 TYR A1110 PHE 0.015 0.001 PHE A 911 TRP 0.016 0.001 TRP A1064 HIS 0.009 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00367 (10568) covalent geometry : angle 0.55422 (14272) hydrogen bonds : bond 0.04263 ( 266) hydrogen bonds : angle 4.63863 ( 741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.283 Fit side-chains REVERT: A 1 MET cc_start: 0.6465 (mmp) cc_final: 0.4690 (ptt) REVERT: A 109 MET cc_start: 0.5251 (mtp) cc_final: 0.3772 (mtm) REVERT: A 247 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8213 (t0) REVERT: A 608 ASN cc_start: 0.8691 (t0) cc_final: 0.8300 (t0) REVERT: A 641 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8686 (tp) REVERT: A 691 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8220 (p0) REVERT: A 863 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6678 (pp20) REVERT: A 1031 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7414 (mtm-85) REVERT: A 1294 TRP cc_start: 0.8786 (t60) cc_final: 0.8136 (t60) REVERT: A 1487 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8401 (mtmm) outliers start: 45 outliers final: 32 residues processed: 135 average time/residue: 0.0993 time to fit residues: 19.1009 Evaluate side-chains 135 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1487 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 80 HIS A 247 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110760 restraints weight = 14145.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.104428 restraints weight = 15102.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105990 restraints weight = 19796.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.107036 restraints weight = 12087.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107581 restraints weight = 10345.345| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10568 Z= 0.175 Angle : 0.576 6.584 14272 Z= 0.301 Chirality : 0.044 0.159 1585 Planarity : 0.004 0.052 1821 Dihedral : 6.048 55.579 1425 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 4.02 % Allowed : 22.66 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -3.32 (0.21), residues: 1283 helix: -1.88 (0.20), residues: 579 sheet: -0.16 (0.44), residues: 127 loop : -3.02 (0.21), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1197 TYR 0.012 0.001 TYR A1110 PHE 0.017 0.001 PHE A 911 TRP 0.017 0.001 TRP A1064 HIS 0.005 0.001 HIS A1091 Details of bonding type rmsd covalent geometry : bond 0.00432 (10568) covalent geometry : angle 0.57616 (14272) hydrogen bonds : bond 0.04572 ( 266) hydrogen bonds : angle 4.74934 ( 741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.380 Fit side-chains REVERT: A 26 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7545 (tp-100) REVERT: A 109 MET cc_start: 0.5692 (mtp) cc_final: 0.4759 (mtm) REVERT: A 247 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8298 (t0) REVERT: A 608 ASN cc_start: 0.8749 (t0) cc_final: 0.8339 (t0) REVERT: A 641 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 691 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8205 (p0) REVERT: A 863 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: A 906 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8919 (mtm) REVERT: A 1031 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7456 (mtm-85) REVERT: A 1294 TRP cc_start: 0.8893 (t60) cc_final: 0.8149 (t60) REVERT: A 1487 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8431 (mtmm) outliers start: 46 outliers final: 33 residues processed: 135 average time/residue: 0.0969 time to fit residues: 19.0394 Evaluate side-chains 135 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1487 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 10 optimal weight: 50.0000 chunk 112 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN A 933 GLN A1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113758 restraints weight = 14008.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111759 restraints weight = 21302.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112511 restraints weight = 25223.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113594 restraints weight = 14030.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.114269 restraints weight = 11252.810| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.130 10568 Z= 0.099 Angle : 0.524 7.275 14272 Z= 0.273 Chirality : 0.040 0.155 1585 Planarity : 0.004 0.049 1821 Dihedral : 5.648 56.797 1425 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 2.71 % Allowed : 23.88 % Favored : 73.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % 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: -2.91 (0.21), residues: 1283 helix: -1.57 (0.21), residues: 576 sheet: 0.14 (0.45), residues: 125 loop : -2.79 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 956 TYR 0.013 0.001 TYR A 202 PHE 0.013 0.001 PHE A 911 TRP 0.014 0.001 TRP A1064 HIS 0.003 0.001 HIS A1154 Details of bonding type rmsd covalent geometry : bond 0.00247 (10568) covalent geometry : angle 0.52417 (14272) hydrogen bonds : bond 0.03221 ( 266) hydrogen bonds : angle 4.34313 ( 741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6435 (mmp) cc_final: 0.4589 (ptt) REVERT: A 109 MET cc_start: 0.5124 (mtp) cc_final: 0.3842 (mtm) REVERT: A 608 ASN cc_start: 0.8677 (t0) cc_final: 0.8271 (t0) REVERT: A 641 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 691 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8111 (p0) REVERT: A 859 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: A 938 THR cc_start: 0.9363 (p) cc_final: 0.9119 (t) REVERT: A 952 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 1031 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7335 (mtm-85) REVERT: A 1294 TRP cc_start: 0.8819 (t60) cc_final: 0.8196 (t60) REVERT: A 1487 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8398 (mtmm) outliers start: 31 outliers final: 22 residues processed: 134 average time/residue: 0.0925 time to fit residues: 18.0090 Evaluate side-chains 131 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1502 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114898 restraints weight = 14028.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.112780 restraints weight = 22530.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113388 restraints weight = 25711.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114128 restraints weight = 14811.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114518 restraints weight = 12262.265| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 10568 Z= 0.142 Angle : 0.559 6.691 14272 Z= 0.291 Chirality : 0.042 0.154 1585 Planarity : 0.004 0.050 1821 Dihedral : 5.582 57.499 1423 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 2.80 % Allowed : 24.15 % Favored : 73.05 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % 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: -2.86 (0.21), residues: 1283 helix: -1.50 (0.21), residues: 577 sheet: 0.05 (0.44), residues: 127 loop : -2.78 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 956 TYR 0.010 0.001 TYR A1071 PHE 0.015 0.001 PHE A 911 TRP 0.017 0.001 TRP A1064 HIS 0.005 0.001 HIS A1091 Details of bonding type rmsd covalent geometry : bond 0.00358 (10568) covalent geometry : angle 0.55850 (14272) hydrogen bonds : bond 0.03971 ( 266) hydrogen bonds : angle 4.46843 ( 741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.391 Fit side-chains REVERT: A 109 MET cc_start: 0.5029 (mtp) cc_final: 0.3574 (mtm) REVERT: A 608 ASN cc_start: 0.8728 (t0) cc_final: 0.8316 (t0) REVERT: A 641 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8606 (tp) REVERT: A 691 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8249 (p0) REVERT: A 863 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6859 (pp20) REVERT: A 906 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8909 (mtm) REVERT: A 952 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8940 (p) REVERT: A 1031 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7346 (mtm-85) REVERT: A 1294 TRP cc_start: 0.8783 (t60) cc_final: 0.8206 (t60) REVERT: A 1487 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8385 (mtmm) REVERT: A 1497 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8343 (ttt180) outliers start: 32 outliers final: 21 residues processed: 121 average time/residue: 0.1043 time to fit residues: 18.1772 Evaluate side-chains 124 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 71 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 734 HIS A 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115830 restraints weight = 13969.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.113283 restraints weight = 23040.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114024 restraints weight = 24448.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115086 restraints weight = 14797.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115471 restraints weight = 11919.539| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 10568 Z= 0.116 Angle : 0.538 8.746 14272 Z= 0.279 Chirality : 0.041 0.163 1585 Planarity : 0.004 0.049 1821 Dihedral : 5.434 58.432 1423 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 2.45 % Allowed : 24.85 % Favored : 72.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % 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: -2.69 (0.22), residues: 1283 helix: -1.31 (0.21), residues: 576 sheet: 0.15 (0.44), residues: 134 loop : -2.79 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 956 TYR 0.012 0.001 TYR A 202 PHE 0.014 0.001 PHE A 911 TRP 0.016 0.001 TRP A1064 HIS 0.004 0.001 HIS A1091 Details of bonding type rmsd covalent geometry : bond 0.00301 (10568) covalent geometry : angle 0.53753 (14272) hydrogen bonds : bond 0.03475 ( 266) hydrogen bonds : angle 4.30376 ( 741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.4937 (mtp) cc_final: 0.3579 (mtm) REVERT: A 608 ASN cc_start: 0.8704 (t0) cc_final: 0.8313 (t0) REVERT: A 641 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 691 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8211 (p0) REVERT: A 863 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6816 (pp20) REVERT: A 906 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8900 (mtm) REVERT: A 952 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 1031 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7364 (mtm-85) REVERT: A 1294 TRP cc_start: 0.8781 (t60) cc_final: 0.8201 (t60) REVERT: A 1487 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8411 (mtmm) REVERT: A 1497 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8338 (ttt180) outliers start: 28 outliers final: 19 residues processed: 125 average time/residue: 0.1066 time to fit residues: 18.8492 Evaluate side-chains 127 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1179 VAL Chi-restraints excluded: chain A residue 1184 GLU Chi-restraints excluded: chain A residue 1298 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 734 HIS A 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.148178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114721 restraints weight = 14072.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113150 restraints weight = 21744.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113775 restraints weight = 23027.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114529 restraints weight = 13968.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115093 restraints weight = 11118.156| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 10568 Z= 0.113 Angle : 0.530 7.392 14272 Z= 0.276 Chirality : 0.041 0.161 1585 Planarity : 0.004 0.049 1821 Dihedral : 5.307 59.129 1421 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.54 % Allowed : 24.50 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: -2.55 (0.22), residues: 1283 helix: -1.14 (0.21), residues: 577 sheet: 0.20 (0.44), residues: 134 loop : -2.77 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 823 TYR 0.009 0.001 TYR A1110 PHE 0.013 0.001 PHE A 911 TRP 0.016 0.001 TRP A1064 HIS 0.007 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00286 (10568) covalent geometry : angle 0.53024 (14272) hydrogen bonds : bond 0.03442 ( 266) hydrogen bonds : angle 4.24607 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.77 seconds wall clock time: 25 minutes 3.45 seconds (1503.45 seconds total)