Starting phenix.real_space_refine on Wed Mar 4 12:10:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ty8_20581/03_2026/6ty8_20581.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ty8_20581/03_2026/6ty8_20581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ty8_20581/03_2026/6ty8_20581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ty8_20581/03_2026/6ty8_20581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ty8_20581/03_2026/6ty8_20581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ty8_20581/03_2026/6ty8_20581.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 53 5.16 5 C 8653 2.51 5 N 2323 2.21 5 O 2575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13607 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9571 Classifications: {'peptide': 1196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 1155} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 479} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.24 Number of scatterers: 13607 At special positions: 0 Unit cell: (105.138, 147.618, 88.146, 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 53 16.00 P 3 15.00 O 2575 8.00 N 2323 7.00 C 8653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 561.7 milliseconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 15 sheets defined 52.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 removed outlier: 3.541A pdb=" N ASN A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 9' Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 19 through 36 removed outlier: 3.637A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.522A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.744A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.988A pdb=" N LEU A 112 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.540A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.166A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.857A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.582A pdb=" N GLU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.603A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.594A pdb=" N SER A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.836A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 410 removed outlier: 4.092A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.717A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.658A pdb=" N SER A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 572 removed outlier: 3.563A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.959A pdb=" N ALA A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 3.749A pdb=" N HIS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.546A pdb=" N LEU A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 739 removed outlier: 3.779A pdb=" N ARG A 738 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 739 " --> pdb=" O ALA A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 735 through 739' Processing helix chain 'A' and resid 752 through 767 Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.684A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 833 through 839 removed outlier: 3.544A pdb=" N LEU A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 4.052A pdb=" N TYR A 870 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 871 " --> pdb=" O GLY A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 867 through 871' Processing helix chain 'A' and resid 872 through 879 removed outlier: 3.976A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.918A pdb=" N GLN A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.689A pdb=" N LEU A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 911 Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'A' and resid 932 through 939 removed outlier: 4.167A pdb=" N GLN A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 959 removed outlier: 3.700A pdb=" N ARG A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 980 removed outlier: 3.775A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 980 " --> pdb=" O LYS A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.723A pdb=" N ARG A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1020 removed outlier: 3.750A pdb=" N ALA A1018 " --> pdb=" O PRO A1015 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1019 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 removed outlier: 4.208A pdb=" N HIS A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A1040 " --> pdb=" O HIS A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1040' Processing helix chain 'A' and resid 1053 through 1062 Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 3.599A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1103 Processing helix chain 'A' and resid 1106 through 1114 Processing helix chain 'A' and resid 1117 through 1135 removed outlier: 3.709A pdb=" N GLY A1122 " --> pdb=" O PRO A1118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1160 removed outlier: 3.518A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1172 removed outlier: 4.144A pdb=" N SER A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1189 removed outlier: 3.762A pdb=" N TYR A1178 " --> pdb=" O CYS A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1211 Processing helix chain 'A' and resid 1214 through 1219 removed outlier: 3.605A pdb=" N ILE A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.784A pdb=" N TYR B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 63 removed outlier: 4.030A pdb=" N SER B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.548A pdb=" N TYR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 4.261A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.773A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.549A pdb=" N PHE B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.854A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.868A pdb=" N PHE B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.068A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 441 through 461 removed outlier: 3.631A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 512 through 520 removed outlier: 3.733A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 538 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.700A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.571A pdb=" N LYS A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.707A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.600A pdb=" N SER A 380 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER A 374 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 477 through 479 removed outlier: 3.775A pdb=" N VAL A 477 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 547 removed outlier: 6.394A pdb=" N ASP A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE A 677 " --> pdb=" O ASP A 681 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET A 683 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 675 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A 685 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 624 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=AB1, first strand: chain 'A' and resid 813 through 816 removed outlier: 4.555A pdb=" N THR A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 831 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 992 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 797 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1022 through 1030 removed outlier: 4.666A pdb=" N ARG A1197 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AB4, first strand: chain 'B' and resid 204 through 208 removed outlier: 6.133A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 297 through 299 removed outlier: 6.619A pdb=" N LEU B 257 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 316 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR B 259 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.586A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR B 504 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1650 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: 3.04 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2227 1.31 - 1.43: 3836 1.43 - 1.56: 7737 1.56 - 1.68: 9 1.68 - 1.81: 94 Bond restraints: 13903 Sorted by residual: bond pdb=" C1B GTA A1301 " pdb=" C2B GTA A1301 " ideal model delta sigma weight residual 1.530 1.303 0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1B GTA A1301 " pdb=" O4B GTA A1301 " ideal model delta sigma weight residual 1.395 1.619 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3A GTA A1301 " pdb=" C4A GTA A1301 " ideal model delta sigma weight residual 1.525 1.346 0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" C4A GTA A1301 " pdb=" O4A GTA A1301 " ideal model delta sigma weight residual 1.433 1.605 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C4 GTA A1301 " pdb=" N3 GTA A1301 " ideal model delta sigma weight residual 1.330 1.488 -0.158 2.00e-02 2.50e+03 6.21e+01 ... (remaining 13898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 18744 4.31 - 8.62: 82 8.62 - 12.93: 10 12.93 - 17.24: 4 17.24 - 21.56: 2 Bond angle restraints: 18842 Sorted by residual: angle pdb=" N GLU A1138 " pdb=" CA GLU A1138 " pdb=" C GLU A1138 " ideal model delta sigma weight residual 110.24 120.83 -10.59 1.41e+00 5.03e-01 5.64e+01 angle pdb=" N1C GTA A1301 " pdb=" C6C GTA A1301 " pdb=" N6C GTA A1301 " ideal model delta sigma weight residual 119.40 97.84 21.56 3.00e+00 1.11e-01 5.16e+01 angle pdb=" N ILE B 498 " pdb=" CA ILE B 498 " pdb=" C ILE B 498 " ideal model delta sigma weight residual 106.88 117.60 -10.72 1.52e+00 4.33e-01 4.97e+01 angle pdb=" N THR B 497 " pdb=" CA THR B 497 " pdb=" C THR B 497 " ideal model delta sigma weight residual 111.36 118.76 -7.40 1.09e+00 8.42e-01 4.61e+01 angle pdb=" C5C GTA A1301 " pdb=" C6C GTA A1301 " pdb=" N6C GTA A1301 " ideal model delta sigma weight residual 122.62 142.09 -19.47 3.00e+00 1.11e-01 4.21e+01 ... (remaining 18837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.96: 8255 29.96 - 59.93: 104 59.93 - 89.89: 8 89.89 - 119.86: 0 119.86 - 149.82: 1 Dihedral angle restraints: 8368 sinusoidal: 3378 harmonic: 4990 Sorted by residual: dihedral pdb=" CA THR A 347 " pdb=" C THR A 347 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LEU A 767 " pdb=" C LEU A 767 " pdb=" N LEU A 768 " pdb=" CA LEU A 768 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ILE A 249 " pdb=" C ILE A 249 " pdb=" N LYS A 250 " pdb=" CA LYS A 250 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 8365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1871 0.083 - 0.165: 210 0.165 - 0.248: 13 0.248 - 0.331: 3 0.331 - 0.414: 4 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CA ASP A 483 " pdb=" N ASP A 483 " pdb=" C ASP A 483 " pdb=" CB ASP A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB VAL A 548 " pdb=" CA VAL A 548 " pdb=" CG1 VAL A 548 " pdb=" CG2 VAL A 548 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 2098 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " -0.025 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP A 606 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 363 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C GLN A 363 " 0.054 2.00e-02 2.50e+03 pdb=" O GLN A 363 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 364 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 769 " -0.012 2.00e-02 2.50e+03 1.88e-02 6.20e+00 pdb=" CG PHE A 769 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 769 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 769 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 769 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 769 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 769 " 0.001 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1521 2.75 - 3.29: 12571 3.29 - 3.82: 21974 3.82 - 4.36: 27146 4.36 - 4.90: 46294 Nonbonded interactions: 109506 Sorted by model distance: nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR B 16 " pdb=" OD2 ASP B 161 " model vdw 2.319 3.040 nonbonded pdb=" O SER A1152 " pdb=" OH TYR A1183 " model vdw 2.322 3.040 nonbonded pdb=" O ILE A 202 " pdb=" OG1 THR A 205 " model vdw 2.324 3.040 nonbonded pdb=" O CYS A 574 " pdb=" ND2 ASN A 603 " model vdw 2.326 3.120 ... (remaining 109501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:9.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.008 0.227 13903 Z= 0.371 Angle : 1.029 21.556 18842 Z= 0.564 Chirality : 0.057 0.414 2101 Planarity : 0.006 0.059 2400 Dihedral : 10.373 149.824 5160 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.91 % Rotamer: Outliers : 0.75 % Allowed : 1.90 % Favored : 97.35 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.16), residues: 1684 helix: -2.34 (0.13), residues: 820 sheet: -1.47 (0.39), residues: 150 loop : -1.86 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1175 TYR 0.030 0.003 TYR A 900 PHE 0.042 0.004 PHE A 769 TRP 0.057 0.004 TRP A 606 HIS 0.018 0.003 HIS B 490 Details of bonding type rmsd covalent geometry : bond 0.00810 (13903) covalent geometry : angle 1.02883 (18842) hydrogen bonds : bond 0.15528 ( 571) hydrogen bonds : angle 6.68064 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 424 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ASP cc_start: 0.7298 (p0) cc_final: 0.6961 (p0) REVERT: A 551 MET cc_start: 0.8024 (ttp) cc_final: 0.7783 (ttt) REVERT: A 809 SER cc_start: 0.8327 (t) cc_final: 0.8106 (p) REVERT: A 877 ASP cc_start: 0.8426 (t0) cc_final: 0.8221 (t0) REVERT: A 926 SER cc_start: 0.3976 (OUTLIER) cc_final: 0.3367 (p) outliers start: 11 outliers final: 3 residues processed: 430 average time/residue: 0.7371 time to fit residues: 340.1134 Evaluate side-chains 236 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain B residue 497 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 126 HIS A 134 HIS A 164 ASN A 274 GLN A 486 GLN A 514 ASN A 617 GLN A 648 HIS A 880 ASN A 887 GLN A1136 ASN A1193 ASN B 9 HIS B 212 ASN B 542 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.091994 restraints weight = 18425.568| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.66 r_work: 0.2798 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13903 Z= 0.124 Angle : 0.535 11.188 18842 Z= 0.282 Chirality : 0.041 0.153 2101 Planarity : 0.004 0.049 2400 Dihedral : 7.307 111.029 1945 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.66 % Allowed : 14.72 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1684 helix: -0.57 (0.17), residues: 811 sheet: -1.33 (0.39), residues: 143 loop : -1.09 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1197 TYR 0.015 0.002 TYR A 242 PHE 0.013 0.001 PHE A 45 TRP 0.025 0.002 TRP A 606 HIS 0.006 0.001 HIS A1039 Details of bonding type rmsd covalent geometry : bond 0.00281 (13903) covalent geometry : angle 0.53499 (18842) hydrogen bonds : bond 0.03865 ( 571) hydrogen bonds : angle 4.85646 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9106 (mttt) REVERT: A 54 ASP cc_start: 0.8337 (t70) cc_final: 0.8082 (t0) REVERT: A 364 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7549 (mtm-85) REVERT: A 479 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7465 (mtp180) REVERT: A 641 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8208 (ttp-170) REVERT: A 809 SER cc_start: 0.8716 (t) cc_final: 0.8306 (p) REVERT: A 926 SER cc_start: 0.4010 (OUTLIER) cc_final: 0.3304 (p) REVERT: A 957 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8535 (ptmm) REVERT: A 978 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: A 1028 ASP cc_start: 0.8334 (t0) cc_final: 0.8042 (t0) REVERT: A 1079 ILE cc_start: 0.8536 (mp) cc_final: 0.8305 (mt) REVERT: A 1080 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7924 (mtt180) REVERT: B 43 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 136 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6791 (mtmm) outliers start: 54 outliers final: 17 residues processed: 266 average time/residue: 0.7302 time to fit residues: 209.9207 Evaluate side-chains 234 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 497 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 51 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 114 ASN A 189 GLN A 274 GLN A1084 HIS A1193 ASN B 174 GLN B 393 ASN B 542 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.082312 restraints weight = 18756.259| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.65 r_work: 0.2659 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13903 Z= 0.239 Angle : 0.614 9.009 18842 Z= 0.322 Chirality : 0.045 0.175 2101 Planarity : 0.005 0.047 2400 Dihedral : 6.680 99.429 1942 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.02 % Allowed : 14.11 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 1684 helix: 0.09 (0.18), residues: 810 sheet: -1.06 (0.37), residues: 160 loop : -0.95 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 377 TYR 0.030 0.002 TYR B 13 PHE 0.020 0.002 PHE A 206 TRP 0.031 0.002 TRP A 606 HIS 0.010 0.002 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00586 (13903) covalent geometry : angle 0.61440 (18842) hydrogen bonds : bond 0.04746 ( 571) hydrogen bonds : angle 4.71841 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8136 (p0) REVERT: A 319 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 364 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7812 (mtm-85) REVERT: A 532 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9058 (mtt) REVERT: A 703 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8968 (tp) REVERT: A 706 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8586 (tt0) REVERT: A 809 SER cc_start: 0.9041 (t) cc_final: 0.8743 (p) REVERT: A 957 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8680 (ptmm) REVERT: A 978 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: A 1028 ASP cc_start: 0.8316 (t0) cc_final: 0.7952 (t0) REVERT: A 1080 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7886 (mtt180) REVERT: B 43 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 404 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: B 413 ASP cc_start: 0.8414 (p0) cc_final: 0.8191 (p0) REVERT: B 443 ARG cc_start: 0.6129 (mpt180) cc_final: 0.5519 (mpt180) REVERT: B 555 ARG cc_start: 0.8255 (ttm110) cc_final: 0.8054 (ttp-170) outliers start: 74 outliers final: 29 residues processed: 258 average time/residue: 0.6867 time to fit residues: 191.8754 Evaluate side-chains 236 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 189 GLN A1084 HIS B 63 HIS B 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.103040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.084591 restraints weight = 18718.432| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.66 r_work: 0.2703 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13903 Z= 0.108 Angle : 0.486 10.228 18842 Z= 0.256 Chirality : 0.040 0.163 2101 Planarity : 0.003 0.045 2400 Dihedral : 6.122 89.208 1940 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.60 % Allowed : 16.21 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1684 helix: 0.63 (0.19), residues: 806 sheet: -0.88 (0.38), residues: 156 loop : -0.66 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.012 0.001 TYR B 13 PHE 0.012 0.001 PHE A 902 TRP 0.014 0.001 TRP A 606 HIS 0.004 0.001 HIS A1039 Details of bonding type rmsd covalent geometry : bond 0.00253 (13903) covalent geometry : angle 0.48648 (18842) hydrogen bonds : bond 0.03338 ( 571) hydrogen bonds : angle 4.44963 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8856 (mtm180) cc_final: 0.8645 (mtm180) REVERT: A 319 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 703 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8949 (tp) REVERT: A 706 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8366 (mt-10) REVERT: A 745 GLU cc_start: 0.8129 (pm20) cc_final: 0.7877 (pt0) REVERT: A 809 SER cc_start: 0.8979 (t) cc_final: 0.8675 (p) REVERT: A 922 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8268 (ttpt) REVERT: A 957 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8623 (ptmm) REVERT: A 978 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: A 1028 ASP cc_start: 0.8311 (t0) cc_final: 0.7934 (t0) REVERT: A 1080 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7776 (mtt180) REVERT: A 1173 GLN cc_start: 0.7074 (mt0) cc_final: 0.6538 (mm-40) REVERT: B 43 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7697 (mp) REVERT: B 241 LYS cc_start: 0.8553 (tptm) cc_final: 0.8139 (tppt) REVERT: B 404 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: B 413 ASP cc_start: 0.8441 (p0) cc_final: 0.7759 (t0) REVERT: B 443 ARG cc_start: 0.5938 (mpt180) cc_final: 0.5329 (mpt180) outliers start: 53 outliers final: 26 residues processed: 237 average time/residue: 0.7555 time to fit residues: 192.4815 Evaluate side-chains 229 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1080 ARG Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 189 GLN A 486 GLN A 807 ASN A 939 GLN B 63 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.081484 restraints weight = 18781.688| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.62 r_work: 0.2699 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13903 Z= 0.235 Angle : 0.586 9.137 18842 Z= 0.305 Chirality : 0.045 0.190 2101 Planarity : 0.004 0.042 2400 Dihedral : 6.229 79.559 1940 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.27 % Allowed : 16.01 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1684 helix: 0.63 (0.18), residues: 810 sheet: -0.92 (0.37), residues: 158 loop : -0.67 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 377 TYR 0.026 0.002 TYR B 13 PHE 0.020 0.002 PHE A 206 TRP 0.022 0.002 TRP A 606 HIS 0.007 0.002 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00576 (13903) covalent geometry : angle 0.58645 (18842) hydrogen bonds : bond 0.04450 ( 571) hydrogen bonds : angle 4.62394 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: A 66 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (mm-40) REVERT: A 319 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 479 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7628 (mtp180) REVERT: A 703 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 706 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8518 (mt-10) REVERT: A 809 SER cc_start: 0.8952 (t) cc_final: 0.8655 (p) REVERT: A 957 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8674 (ptmm) REVERT: A 978 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: A 1028 ASP cc_start: 0.8305 (t0) cc_final: 0.7872 (t0) REVERT: B 11 LYS cc_start: 0.9075 (mptp) cc_final: 0.8755 (mmtm) REVERT: B 14 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: B 43 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 136 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7209 (mptp) REVERT: B 199 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7730 (ttp-110) REVERT: B 241 LYS cc_start: 0.8559 (tptm) cc_final: 0.8203 (tppt) REVERT: B 413 ASP cc_start: 0.8519 (p0) cc_final: 0.7913 (t0) REVERT: B 443 ARG cc_start: 0.6481 (mpt180) cc_final: 0.5581 (mpt180) outliers start: 63 outliers final: 36 residues processed: 248 average time/residue: 0.7564 time to fit residues: 202.0028 Evaluate side-chains 241 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 486 GLN A 887 GLN A1084 HIS B 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.084645 restraints weight = 18586.623| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.63 r_work: 0.2690 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13903 Z= 0.106 Angle : 0.481 10.689 18842 Z= 0.253 Chirality : 0.040 0.167 2101 Planarity : 0.003 0.040 2400 Dihedral : 5.840 74.217 1940 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.27 % Allowed : 17.30 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1684 helix: 0.94 (0.19), residues: 806 sheet: -0.83 (0.38), residues: 153 loop : -0.48 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.012 0.001 TYR A1183 PHE 0.013 0.001 PHE A 206 TRP 0.013 0.001 TRP A 606 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00250 (13903) covalent geometry : angle 0.48110 (18842) hydrogen bonds : bond 0.03217 ( 571) hydrogen bonds : angle 4.43111 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: A 37 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (ttp80) REVERT: A 319 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 479 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7903 (mmm160) REVERT: A 703 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8954 (tp) REVERT: A 706 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8393 (mt-10) REVERT: A 809 SER cc_start: 0.8990 (t) cc_final: 0.8675 (p) REVERT: A 922 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8244 (ttpt) REVERT: A 957 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8651 (ptmm) REVERT: A 978 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: A 1028 ASP cc_start: 0.8319 (t0) cc_final: 0.7843 (t0) REVERT: B 11 LYS cc_start: 0.9050 (mptp) cc_final: 0.8785 (mmtm) REVERT: B 43 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 241 LYS cc_start: 0.8509 (tptm) cc_final: 0.8127 (tppt) REVERT: B 413 ASP cc_start: 0.8429 (p0) cc_final: 0.7926 (t0) REVERT: B 443 ARG cc_start: 0.6226 (mpt180) cc_final: 0.5352 (mpt180) REVERT: B 452 MET cc_start: 0.9273 (tpt) cc_final: 0.8922 (tpt) outliers start: 63 outliers final: 28 residues processed: 240 average time/residue: 0.7344 time to fit residues: 189.8629 Evaluate side-chains 225 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 140 optimal weight: 0.2980 chunk 19 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.080677 restraints weight = 18809.134| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.63 r_work: 0.2630 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13903 Z= 0.178 Angle : 0.535 9.710 18842 Z= 0.279 Chirality : 0.043 0.217 2101 Planarity : 0.004 0.040 2400 Dihedral : 5.809 69.560 1940 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.00 % Allowed : 17.71 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1684 helix: 0.95 (0.19), residues: 807 sheet: -0.87 (0.37), residues: 163 loop : -0.46 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 950 TYR 0.017 0.002 TYR B 13 PHE 0.017 0.001 PHE A 206 TRP 0.012 0.001 TRP A 606 HIS 0.006 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00436 (13903) covalent geometry : angle 0.53479 (18842) hydrogen bonds : bond 0.03864 ( 571) hydrogen bonds : angle 4.50448 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: A 37 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8523 (ttp80) REVERT: A 319 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 479 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7978 (mmm160) REVERT: A 703 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9004 (tp) REVERT: A 706 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8475 (mt-10) REVERT: A 809 SER cc_start: 0.8954 (t) cc_final: 0.8641 (p) REVERT: A 859 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: A 922 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8252 (ttpt) REVERT: A 957 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8681 (ptmm) REVERT: A 978 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6804 (mp10) REVERT: A 1014 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (ptp) REVERT: A 1028 ASP cc_start: 0.8346 (t0) cc_final: 0.7827 (t0) REVERT: B 11 LYS cc_start: 0.9098 (mptp) cc_final: 0.8815 (mmtm) REVERT: B 43 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 136 LYS cc_start: 0.7310 (mmtm) cc_final: 0.6955 (mttp) REVERT: B 199 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7752 (ttp-110) REVERT: B 241 LYS cc_start: 0.8553 (tptm) cc_final: 0.8176 (tppt) REVERT: B 413 ASP cc_start: 0.8430 (p0) cc_final: 0.7946 (t0) REVERT: B 443 ARG cc_start: 0.6437 (mpt180) cc_final: 0.5548 (mpt180) outliers start: 59 outliers final: 33 residues processed: 226 average time/residue: 0.7575 time to fit residues: 184.2465 Evaluate side-chains 227 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 957 LYS Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1171 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.100024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.081871 restraints weight = 18633.868| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.61 r_work: 0.2668 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13903 Z= 0.142 Angle : 0.509 10.198 18842 Z= 0.267 Chirality : 0.041 0.221 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.617 65.321 1940 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.66 % Allowed : 18.18 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1684 helix: 1.07 (0.19), residues: 806 sheet: -0.51 (0.40), residues: 143 loop : -0.42 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 950 TYR 0.015 0.001 TYR A1183 PHE 0.015 0.001 PHE A 206 TRP 0.011 0.001 TRP B 260 HIS 0.006 0.001 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00345 (13903) covalent geometry : angle 0.50902 (18842) hydrogen bonds : bond 0.03495 ( 571) hydrogen bonds : angle 4.44306 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: A 37 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8500 (ttp80) REVERT: A 199 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8702 (m) REVERT: A 319 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 479 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7961 (mmm160) REVERT: A 703 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9015 (tp) REVERT: A 706 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8428 (mt-10) REVERT: A 809 SER cc_start: 0.8927 (t) cc_final: 0.8627 (p) REVERT: A 922 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8251 (ttpt) REVERT: A 978 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: B 11 LYS cc_start: 0.9088 (mptp) cc_final: 0.8807 (mmtm) REVERT: B 43 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 136 LYS cc_start: 0.7315 (mmtm) cc_final: 0.6913 (mttp) REVERT: B 199 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7742 (ttp-110) REVERT: B 241 LYS cc_start: 0.8503 (tptm) cc_final: 0.8148 (tppt) REVERT: B 413 ASP cc_start: 0.8416 (p0) cc_final: 0.8001 (t0) REVERT: B 443 ARG cc_start: 0.6336 (mpt180) cc_final: 0.5478 (mpt180) outliers start: 54 outliers final: 32 residues processed: 223 average time/residue: 0.7683 time to fit residues: 184.6054 Evaluate side-chains 224 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 117 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 18 optimal weight: 0.0670 chunk 142 optimal weight: 10.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.098058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.079600 restraints weight = 18958.268| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.69 r_work: 0.2614 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13903 Z= 0.188 Angle : 0.555 9.842 18842 Z= 0.288 Chirality : 0.043 0.221 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.637 61.863 1940 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.60 % Allowed : 18.59 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1684 helix: 1.04 (0.19), residues: 806 sheet: -0.43 (0.40), residues: 141 loop : -0.46 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 950 TYR 0.016 0.002 TYR A1183 PHE 0.018 0.002 PHE A 206 TRP 0.012 0.001 TRP A 606 HIS 0.006 0.001 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00459 (13903) covalent geometry : angle 0.55541 (18842) hydrogen bonds : bond 0.03942 ( 571) hydrogen bonds : angle 4.52111 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: A 37 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8379 (ttp80) REVERT: A 199 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8646 (m) REVERT: A 319 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 479 ARG cc_start: 0.8241 (mmm160) cc_final: 0.8030 (mmm160) REVERT: A 703 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 706 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8440 (mt-10) REVERT: A 809 SER cc_start: 0.8900 (t) cc_final: 0.8589 (p) REVERT: A 922 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8229 (ttpt) REVERT: A 978 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6714 (mp10) REVERT: A 1014 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8106 (ptp) REVERT: B 11 LYS cc_start: 0.9108 (mptp) cc_final: 0.8822 (mmtm) REVERT: B 43 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7858 (mp) REVERT: B 136 LYS cc_start: 0.7250 (mmtm) cc_final: 0.6868 (mttp) REVERT: B 199 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7769 (ttp-110) REVERT: B 241 LYS cc_start: 0.8523 (tptm) cc_final: 0.8135 (tppt) REVERT: B 413 ASP cc_start: 0.8397 (p0) cc_final: 0.8011 (t0) REVERT: B 443 ARG cc_start: 0.6445 (mpt180) cc_final: 0.5579 (mpt180) REVERT: B 502 ASP cc_start: 0.8094 (t0) cc_final: 0.7771 (t0) outliers start: 53 outliers final: 35 residues processed: 218 average time/residue: 0.7849 time to fit residues: 184.4069 Evaluate side-chains 227 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 189 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 63 HIS B 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.081021 restraints weight = 18851.957| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.62 r_work: 0.2662 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13903 Z= 0.153 Angle : 0.529 10.207 18842 Z= 0.274 Chirality : 0.042 0.215 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.506 59.234 1940 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.12 % Allowed : 19.06 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1684 helix: 1.11 (0.19), residues: 806 sheet: -0.46 (0.40), residues: 143 loop : -0.41 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 950 TYR 0.015 0.001 TYR A1183 PHE 0.016 0.001 PHE A 206 TRP 0.011 0.001 TRP A 606 HIS 0.006 0.001 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00372 (13903) covalent geometry : angle 0.52917 (18842) hydrogen bonds : bond 0.03595 ( 571) hydrogen bonds : angle 4.47500 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: A 37 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: A 199 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8719 (m) REVERT: A 319 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 703 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9016 (tp) REVERT: A 706 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8443 (mt-10) REVERT: A 809 SER cc_start: 0.8898 (t) cc_final: 0.8612 (p) REVERT: A 922 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8283 (ttpt) REVERT: A 978 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: A 1014 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8095 (ptp) REVERT: B 11 LYS cc_start: 0.9105 (mptp) cc_final: 0.8835 (mmtm) REVERT: B 43 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 136 LYS cc_start: 0.7383 (mmtm) cc_final: 0.7072 (mttp) REVERT: B 199 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7765 (ttp-110) REVERT: B 241 LYS cc_start: 0.8526 (tptm) cc_final: 0.8163 (tppt) REVERT: B 413 ASP cc_start: 0.8353 (p0) cc_final: 0.8033 (t0) REVERT: B 443 ARG cc_start: 0.6480 (mpt180) cc_final: 0.5591 (mpt180) REVERT: B 502 ASP cc_start: 0.8121 (t0) cc_final: 0.7840 (t0) outliers start: 46 outliers final: 30 residues processed: 213 average time/residue: 0.7853 time to fit residues: 179.8443 Evaluate side-chains 226 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 114 optimal weight: 0.0030 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.099575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.081497 restraints weight = 18859.232| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.62 r_work: 0.2670 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13903 Z= 0.146 Angle : 0.534 10.854 18842 Z= 0.276 Chirality : 0.042 0.235 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.432 57.639 1940 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.39 % Allowed : 18.79 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1684 helix: 1.15 (0.19), residues: 806 sheet: -0.44 (0.40), residues: 143 loop : -0.40 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 950 TYR 0.015 0.001 TYR A1183 PHE 0.016 0.001 PHE A 206 TRP 0.010 0.001 TRP A 606 HIS 0.006 0.001 HIS A1036 Details of bonding type rmsd covalent geometry : bond 0.00353 (13903) covalent geometry : angle 0.53399 (18842) hydrogen bonds : bond 0.03529 ( 571) hydrogen bonds : angle 4.45411 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4859.14 seconds wall clock time: 83 minutes 29.26 seconds (5009.26 seconds total)