Starting phenix.real_space_refine on Mon Jul 28 08:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y6k_10706/07_2025/6y6k_10706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y6k_10706/07_2025/6y6k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y6k_10706/07_2025/6y6k_10706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y6k_10706/07_2025/6y6k_10706.map" model { file = "/net/cci-nas-00/data/ceres_data/6y6k_10706/07_2025/6y6k_10706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y6k_10706/07_2025/6y6k_10706.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.63, per 1000 atoms: 0.54 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.33 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: 3.28 Time building geometry restraints manager: 2.62 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- 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 : 11.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.003 TRP A 520 HIS 0.008 0.002 HIS A1246 PHE 0.026 0.003 PHE A1010 TYR 0.022 0.003 TYR A1110 ARG 0.003 0.001 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.34222 ( 266) hydrogen bonds : angle 10.34311 ( 741) covalent geometry : bond 0.01170 (10568) covalent geometry : angle 0.99193 (14272) *********************** 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 : 1.035 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: 0.9022 (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: 0.2729 time to fit residues: 54.9754 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 : 1.149 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.0060 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.5694 ------------------------------------------------------------------------------- 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 A 670 GLN A 734 HIS A 799 HIS A 853 ASN A 870 HIS A1203 HIS A1239 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.146932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114854 restraints weight = 13964.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112081 restraints weight = 21914.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.112868 restraints weight = 25352.500| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1903 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= 0.121 Angle : 0.601 8.252 14272 Z= 0.319 Chirality : 0.042 0.141 1585 Planarity : 0.005 0.063 1821 Dihedral : 7.301 61.959 1445 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 3.24 % Allowed : 20.82 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.18), residues: 1283 helix: -3.19 (0.17), residues: 569 sheet: -0.76 (0.44), residues: 125 loop : -3.43 (0.20), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 520 HIS 0.006 0.001 HIS A 870 PHE 0.010 0.001 PHE A1147 TYR 0.011 0.001 TYR A1110 ARG 0.004 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 266) hydrogen bonds : angle 5.46922 ( 741) covalent geometry : bond 0.00253 (10568) covalent geometry : angle 0.60123 (14272) *********************** 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 151 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.162 Fit side-chains REVERT: A 598 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8248 (t80) REVERT: A 608 ASN cc_start: 0.8615 (t0) cc_final: 0.8256 (t0) REVERT: A 636 LYS cc_start: 0.8894 (tttt) cc_final: 0.8621 (tttm) REVERT: A 691 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8139 (p0) REVERT: A 754 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7710 (t80) REVERT: A 863 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6513 (pp20) REVERT: A 956 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7666 (mtm110) REVERT: A 1290 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7894 (mmm160) outliers start: 37 outliers final: 15 residues processed: 149 average time/residue: 0.3890 time to fit residues: 83.4932 Evaluate side-chains 122 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 905 CYS Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 956 ARG Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1056 PHE Chi-restraints excluded: chain A residue 1175 THR 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 115 optimal weight: 0.0370 chunk 126 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 14 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A 865 GLN A 895 GLN A 916 HIS A1035 HIS A1239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.108826 restraints weight = 14345.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110369 restraints weight = 31695.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110463 restraints weight = 19899.837| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10568 Z= 0.276 Angle : 0.688 8.304 14272 Z= 0.361 Chirality : 0.048 0.205 1585 Planarity : 0.005 0.062 1821 Dihedral : 6.980 57.219 1429 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.95 % Favored : 91.97 % Rotamer: Outliers : 3.67 % Allowed : 22.83 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.19), residues: 1283 helix: -2.82 (0.18), residues: 577 sheet: -0.59 (0.45), residues: 122 loop : -3.41 (0.20), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 520 HIS 0.007 0.001 HIS A1190 PHE 0.020 0.002 PHE A1010 TYR 0.015 0.002 TYR A1110 ARG 0.004 0.000 ARG A1582 Details of bonding type rmsd hydrogen bonds : bond 0.06409 ( 266) hydrogen bonds : angle 5.49880 ( 741) covalent geometry : bond 0.00675 (10568) covalent geometry : angle 0.68843 (14272) *********************** 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: 42 poor density : 99 time to evaluate : 1.516 Fit side-chains REVERT: A 1 MET cc_start: 0.6365 (mmp) cc_final: 0.4578 (ptt) REVERT: A 608 ASN cc_start: 0.8691 (t0) cc_final: 0.8286 (t0) REVERT: A 636 LYS cc_start: 0.8974 (tttt) cc_final: 0.8596 (tttm) REVERT: A 781 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: A 863 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: A 956 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7631 (ptt90) REVERT: A 1290 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7952 (mmm160) REVERT: A 1294 TRP cc_start: 0.8754 (t60) cc_final: 0.8229 (t60) outliers start: 42 outliers final: 31 residues processed: 135 average time/residue: 0.2790 time to fit residues: 53.7355 Evaluate side-chains 131 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 SER 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 652 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 684 GLN 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 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 932 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 956 ARG 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 1179 VAL Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1290 ARG 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 69 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 895 GLN A1483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.110920 restraints weight = 14082.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.105202 restraints weight = 14837.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.106292 restraints weight = 20401.032| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10568 Z= 0.147 Angle : 0.574 7.150 14272 Z= 0.303 Chirality : 0.043 0.139 1585 Planarity : 0.004 0.057 1821 Dihedral : 6.570 59.787 1429 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.50 % Allowed : 23.88 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.20), residues: 1283 helix: -2.41 (0.19), residues: 581 sheet: -0.41 (0.44), residues: 127 loop : -3.22 (0.21), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.004 0.001 HIS A1190 PHE 0.016 0.001 PHE A 911 TYR 0.013 0.001 TYR A 202 ARG 0.003 0.000 ARG A1582 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 266) hydrogen bonds : angle 4.91069 ( 741) covalent geometry : bond 0.00355 (10568) covalent geometry : angle 0.57408 (14272) *********************** 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 140 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 1.125 Fit side-chains REVERT: A 109 MET cc_start: 0.5920 (mtp) cc_final: 0.5074 (mtm) REVERT: A 221 LEU cc_start: 0.8216 (mt) cc_final: 0.8009 (mt) REVERT: A 608 ASN cc_start: 0.8658 (t0) cc_final: 0.8286 (t0) REVERT: A 691 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8114 (p0) REVERT: A 863 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6635 (pp20) REVERT: A 956 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7564 (ptt90) REVERT: A 1031 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7498 (mtm-85) REVERT: A 1294 TRP cc_start: 0.8866 (t60) cc_final: 0.8248 (t60) outliers start: 40 outliers final: 26 residues processed: 134 average time/residue: 0.3668 time to fit residues: 71.1355 Evaluate side-chains 123 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 5.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 524 LEU 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 799 HIS 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 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 956 ARG 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110048 restraints weight = 14133.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109074 restraints weight = 29825.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110296 restraints weight = 24763.760| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10568 Z= 0.172 Angle : 0.584 6.892 14272 Z= 0.307 Chirality : 0.043 0.138 1585 Planarity : 0.004 0.056 1821 Dihedral : 6.410 58.914 1427 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 4.11 % Allowed : 23.27 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.21), residues: 1283 helix: -2.19 (0.20), residues: 577 sheet: -0.28 (0.46), residues: 125 loop : -3.14 (0.21), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.005 0.001 HIS A1190 PHE 0.016 0.001 PHE A 911 TYR 0.011 0.001 TYR A1110 ARG 0.003 0.000 ARG A1582 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 266) hydrogen bonds : angle 4.90499 ( 741) covalent geometry : bond 0.00420 (10568) covalent geometry : angle 0.58376 (14272) *********************** 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 144 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 1.198 Fit side-chains REVERT: A 1 MET cc_start: 0.6451 (mmp) cc_final: 0.4720 (ptt) REVERT: A 26 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7588 (tp-100) REVERT: A 608 ASN cc_start: 0.8730 (t0) cc_final: 0.8321 (t0) REVERT: A 691 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8259 (p0) REVERT: A 863 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: A 956 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7545 (ptt90) REVERT: A 1031 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7446 (mtm-85) REVERT: A 1203 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8268 (p90) REVERT: A 1294 TRP cc_start: 0.8762 (t60) cc_final: 0.8245 (t60) outliers start: 47 outliers final: 32 residues processed: 135 average time/residue: 0.2386 time to fit residues: 46.3742 Evaluate side-chains 131 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 365 TRP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 524 LEU 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 774 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 799 HIS 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 906 MET 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 956 ARG 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 1302 LEU Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1597 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.148249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.114258 restraints weight = 13971.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108681 restraints weight = 14358.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109494 restraints weight = 23862.590| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 10568 Z= 0.097 Angle : 0.519 5.977 14272 Z= 0.271 Chirality : 0.040 0.135 1585 Planarity : 0.004 0.051 1821 Dihedral : 5.910 57.066 1427 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.45 % Allowed : 24.67 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.21), residues: 1283 helix: -1.80 (0.20), residues: 572 sheet: -0.01 (0.46), residues: 125 loop : -2.93 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 520 HIS 0.003 0.000 HIS A 993 PHE 0.012 0.001 PHE A 911 TYR 0.009 0.001 TYR A1110 ARG 0.002 0.000 ARG A1582 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 266) hydrogen bonds : angle 4.41205 ( 741) covalent geometry : bond 0.00230 (10568) covalent geometry : angle 0.51897 (14272) *********************** 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 137 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.5641 (mtp) cc_final: 0.4602 (mtm) REVERT: A 221 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 608 ASN cc_start: 0.8694 (t0) cc_final: 0.8302 (t0) REVERT: A 691 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 863 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: A 956 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7484 (ptt90) REVERT: A 1031 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7452 (mtm-85) REVERT: A 1203 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8189 (p90) outliers start: 28 outliers final: 18 residues processed: 132 average time/residue: 0.2103 time to fit residues: 40.3807 Evaluate side-chains 124 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 579 LEU Chi-restraints excluded: chain A residue 600 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 0.0370 chunk 77 optimal weight: 9.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 799 HIS A 895 GLN A1095 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.150081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116153 restraints weight = 14108.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.110408 restraints weight = 14142.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111826 restraints weight = 15258.369| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.111 10568 Z= 0.092 Angle : 0.501 5.943 14272 Z= 0.260 Chirality : 0.039 0.134 1585 Planarity : 0.004 0.049 1821 Dihedral : 5.421 58.000 1425 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.54 % Allowed : 24.67 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.22), residues: 1283 helix: -1.47 (0.21), residues: 576 sheet: 0.11 (0.44), residues: 134 loop : -2.82 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.003 0.000 HIS A1154 PHE 0.013 0.001 PHE A 911 TYR 0.017 0.001 TYR A1471 ARG 0.002 0.000 ARG A1582 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 266) hydrogen bonds : angle 4.10695 ( 741) covalent geometry : bond 0.00228 (10568) covalent geometry : angle 0.50117 (14272) *********************** 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 144 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 2.249 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7633 (tp-100) REVERT: A 109 MET cc_start: 0.5477 (mtp) cc_final: 0.4335 (mtm) REVERT: A 608 ASN cc_start: 0.8591 (t0) cc_final: 0.8208 (t0) REVERT: A 691 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8099 (p0) REVERT: A 952 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8905 (p) REVERT: A 954 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 1182 ASN cc_start: 0.8327 (t0) cc_final: 0.8114 (t0) REVERT: A 1203 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8171 (p90) REVERT: A 1294 TRP cc_start: 0.8865 (t60) cc_final: 0.8249 (t60) REVERT: A 1487 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8415 (mtmm) outliers start: 29 outliers final: 19 residues processed: 138 average time/residue: 0.2250 time to fit residues: 45.3670 Evaluate side-chains 135 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 600 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 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 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 1487 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 97 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 92 optimal weight: 6.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 895 GLN A 933 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118299 restraints weight = 14023.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115302 restraints weight = 22095.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116336 restraints weight = 25825.580| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 10568 Z= 0.099 Angle : 0.504 6.481 14272 Z= 0.262 Chirality : 0.040 0.133 1585 Planarity : 0.004 0.109 1821 Dihedral : 5.256 58.374 1423 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 2.71 % Allowed : 24.41 % Favored : 72.88 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.22), residues: 1283 helix: -1.24 (0.21), residues: 576 sheet: 0.26 (0.44), residues: 134 loop : -2.76 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.003 0.000 HIS A1154 PHE 0.012 0.001 PHE A 911 TYR 0.011 0.001 TYR A 24 ARG 0.005 0.000 ARG A1031 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 266) hydrogen bonds : angle 4.04471 ( 741) covalent geometry : bond 0.00254 (10568) covalent geometry : angle 0.50369 (14272) *********************** 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 138 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7506 (tp-100) REVERT: A 109 MET cc_start: 0.4781 (mtp) cc_final: 0.3223 (mtm) REVERT: A 608 ASN cc_start: 0.8645 (t0) cc_final: 0.8250 (t0) REVERT: A 691 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8218 (p0) REVERT: A 938 THR cc_start: 0.9382 (p) cc_final: 0.9150 (t) REVERT: A 1079 MET cc_start: 0.8170 (mtp) cc_final: 0.7886 (mtm) REVERT: A 1203 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8151 (p90) REVERT: A 1294 TRP cc_start: 0.8759 (t60) cc_final: 0.8238 (t60) REVERT: A 1487 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: A 1497 ARG cc_start: 0.8614 (ttm170) cc_final: 0.8388 (ttt180) outliers start: 31 outliers final: 24 residues processed: 130 average time/residue: 0.2119 time to fit residues: 40.2052 Evaluate side-chains 131 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 600 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 864 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 954 ASN Chi-restraints excluded: chain A residue 990 ASN 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 1302 LEU Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1487 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.111053 restraints weight = 14227.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.105952 restraints weight = 15403.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.107708 restraints weight = 20347.788| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 10568 Z= 0.181 Angle : 0.586 6.803 14272 Z= 0.307 Chirality : 0.044 0.136 1585 Planarity : 0.004 0.069 1821 Dihedral : 5.626 58.552 1423 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 2.54 % Allowed : 24.50 % Favored : 72.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.22), residues: 1283 helix: -1.40 (0.21), residues: 578 sheet: 0.12 (0.44), residues: 127 loop : -2.77 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1294 HIS 0.005 0.001 HIS A1190 PHE 0.017 0.001 PHE A1010 TYR 0.012 0.002 TYR A 202 ARG 0.004 0.000 ARG A1031 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 266) hydrogen bonds : angle 4.49745 ( 741) covalent geometry : bond 0.00453 (10568) covalent geometry : angle 0.58588 (14272) *********************** 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 127 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.093 Fit side-chains REVERT: A 109 MET cc_start: 0.5573 (mtp) cc_final: 0.4524 (mtm) REVERT: A 608 ASN cc_start: 0.8786 (t0) cc_final: 0.8388 (t0) REVERT: A 691 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8205 (p0) REVERT: A 1203 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.8296 (p90) REVERT: A 1294 TRP cc_start: 0.8874 (t60) cc_final: 0.8267 (t60) REVERT: A 1487 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8440 (mtmm) REVERT: A 1497 ARG cc_start: 0.8614 (ttm170) cc_final: 0.8312 (ttt180) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 0.2234 time to fit residues: 38.9081 Evaluate side-chains 121 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP 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 600 SER 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 774 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU 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 1302 LEU Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1487 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112757 restraints weight = 14110.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109041 restraints weight = 20732.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110041 restraints weight = 24657.739| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 10568 Z= 0.141 Angle : 0.552 6.630 14272 Z= 0.288 Chirality : 0.042 0.135 1585 Planarity : 0.004 0.054 1821 Dihedral : 5.568 59.105 1423 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.54 % Allowed : 24.85 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.22), residues: 1283 helix: -1.30 (0.21), residues: 577 sheet: 0.07 (0.43), residues: 134 loop : -2.82 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.004 0.001 HIS A1190 PHE 0.014 0.001 PHE A 911 TYR 0.011 0.001 TYR A1110 ARG 0.007 0.000 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 266) hydrogen bonds : angle 4.36433 ( 741) covalent geometry : bond 0.00357 (10568) covalent geometry : angle 0.55179 (14272) ********************** 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: 29 poor density : 103 time to evaluate : 1.141 Fit side-chains REVERT: A 109 MET cc_start: 0.5006 (mtp) cc_final: 0.3563 (mtm) REVERT: A 608 ASN cc_start: 0.8768 (t0) cc_final: 0.8385 (t0) REVERT: A 691 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8256 (p0) REVERT: A 952 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.9002 (p) REVERT: A 1203 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8256 (p90) REVERT: A 1294 TRP cc_start: 0.8808 (t60) cc_final: 0.8260 (t60) REVERT: A 1487 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8505 (mtmm) REVERT: A 1497 ARG cc_start: 0.8670 (ttm170) cc_final: 0.8367 (ttt180) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.2350 time to fit residues: 40.9716 Evaluate side-chains 127 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 543 ILE Chi-restraints excluded: chain A residue 600 SER 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 774 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 905 CYS Chi-restraints excluded: chain A residue 919 LEU 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 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 1302 LEU Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1408 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 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.0370 chunk 27 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112753 restraints weight = 13999.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109821 restraints weight = 21884.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.110811 restraints weight = 25217.077| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 10568 Z= 0.133 Angle : 0.551 7.474 14272 Z= 0.287 Chirality : 0.042 0.133 1585 Planarity : 0.004 0.064 1821 Dihedral : 5.536 59.510 1423 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 2.89 % Allowed : 24.58 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.22), residues: 1283 helix: -1.23 (0.21), residues: 577 sheet: 0.08 (0.43), residues: 134 loop : -2.80 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1064 HIS 0.004 0.001 HIS A 993 PHE 0.016 0.001 PHE A 911 TYR 0.012 0.001 TYR A 202 ARG 0.006 0.000 ARG A1031 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 266) hydrogen bonds : angle 4.31232 ( 741) covalent geometry : bond 0.00333 (10568) covalent geometry : angle 0.55072 (14272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.03 seconds wall clock time: 62 minutes 4.67 seconds (3724.67 seconds total)