Starting phenix.real_space_refine on Thu Jul 31 14:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ty8_20581/07_2025/6ty8_20581.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ty8_20581/07_2025/6ty8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ty8_20581/07_2025/6ty8_20581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ty8_20581/07_2025/6ty8_20581.map" model { file = "/net/cci-nas-00/data/ceres_data/6ty8_20581/07_2025/6ty8_20581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ty8_20581/07_2025/6ty8_20581.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 19.03, per 1000 atoms: 1.40 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: 7.23 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.51 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: 8.81 Time building geometry restraints manager: 8.02 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: 51.650 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: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 66.910 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:134.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 254.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (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 TRP 0.057 0.004 TRP A 606 HIS 0.018 0.003 HIS B 490 PHE 0.042 0.004 PHE A 769 TYR 0.030 0.003 TYR A 900 ARG 0.013 0.001 ARG A1175 Details of bonding type rmsd hydrogen bonds : bond 0.15528 ( 571) hydrogen bonds : angle 6.68064 ( 1650) covalent geometry : bond 0.00810 (13903) covalent geometry : angle 1.02883 (18842) *********************** 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 : 1.443 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: 0.8105 (p) REVERT: A 877 ASP cc_start: 0.8426 (t0) cc_final: 0.8224 (t0) REVERT: A 926 SER cc_start: 0.3976 (OUTLIER) cc_final: 0.3366 (p) outliers start: 11 outliers final: 3 residues processed: 430 average time/residue: 2.2119 time to fit residues: 1025.3856 Evaluate side-chains 235 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 141 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 152 optimal weight: 0.3980 overall best weight: 3.6844 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.089607 restraints weight = 18505.043| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.66 r_work: 0.2754 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13903 Z= 0.152 Angle : 0.554 11.076 18842 Z= 0.292 Chirality : 0.042 0.155 2101 Planarity : 0.004 0.049 2400 Dihedral : 7.152 106.742 1945 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.00 % Allowed : 14.45 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1684 helix: -0.50 (0.17), residues: 809 sheet: -1.31 (0.39), residues: 143 loop : -1.11 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 606 HIS 0.007 0.001 HIS A1039 PHE 0.015 0.002 PHE A 45 TYR 0.016 0.002 TYR A 242 ARG 0.004 0.001 ARG A1197 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 571) hydrogen bonds : angle 4.81610 ( 1650) covalent geometry : bond 0.00359 (13903) covalent geometry : angle 0.55376 (18842) *********************** 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 291 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9134 (mttt) REVERT: A 54 ASP cc_start: 0.8360 (t70) cc_final: 0.8091 (t0) REVERT: A 364 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7737 (mtm-85) REVERT: A 375 ASN cc_start: 0.8021 (t0) cc_final: 0.7735 (t0) REVERT: A 479 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7774 (mtp180) REVERT: A 809 SER cc_start: 0.8802 (t) cc_final: 0.8454 (p) REVERT: A 926 SER cc_start: 0.4282 (OUTLIER) cc_final: 0.3604 (p) REVERT: A 957 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8546 (ptmm) REVERT: A 978 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6738 (mp10) REVERT: A 1028 ASP cc_start: 0.8304 (t0) cc_final: 0.8010 (t0) REVERT: A 1080 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7917 (mtt180) REVERT: B 43 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7510 (mp) REVERT: B 136 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6725 (mttp) outliers start: 59 outliers final: 22 residues processed: 268 average time/residue: 1.4305 time to fit residues: 415.0015 Evaluate side-chains 240 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 673 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 813 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 958 ILE Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1029 VAL 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 34 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 189 GLN A 274 GLN A 486 GLN A 807 ASN A1084 HIS B 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.082086 restraints weight = 18598.558| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.65 r_work: 0.2688 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13903 Z= 0.228 Angle : 0.600 9.044 18842 Z= 0.313 Chirality : 0.044 0.165 2101 Planarity : 0.005 0.047 2400 Dihedral : 6.568 97.295 1942 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.22 % Allowed : 13.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1684 helix: 0.16 (0.18), residues: 810 sheet: -1.03 (0.37), residues: 156 loop : -0.91 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 606 HIS 0.009 0.002 HIS A1036 PHE 0.019 0.002 PHE A 206 TYR 0.028 0.002 TYR B 13 ARG 0.007 0.001 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 571) hydrogen bonds : angle 4.69924 ( 1650) covalent geometry : bond 0.00557 (13903) covalent geometry : angle 0.59982 (18842) *********************** 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 290 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 213 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8403 (tp-100) REVERT: A 114 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8157 (p0) REVERT: A 319 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 479 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7989 (mmm160) REVERT: A 532 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9104 (mtt) REVERT: A 703 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8958 (tp) REVERT: A 706 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8514 (tt0) REVERT: A 725 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: A 809 SER cc_start: 0.9068 (t) cc_final: 0.8738 (p) REVERT: A 939 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8378 (tp40) REVERT: A 957 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8693 (ptmm) REVERT: A 978 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6681 (mp10) REVERT: A 1028 ASP cc_start: 0.8280 (t0) cc_final: 0.7903 (t0) REVERT: A 1049 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.9061 (mtp) REVERT: A 1080 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7846 (mtt180) REVERT: B 43 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7722 (mp) REVERT: B 404 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: B 413 ASP cc_start: 0.8436 (p0) cc_final: 0.8197 (p0) REVERT: B 443 ARG cc_start: 0.6147 (mpt180) cc_final: 0.5330 (mpt180) outliers start: 77 outliers final: 29 residues processed: 258 average time/residue: 1.4824 time to fit residues: 413.5502 Evaluate side-chains 241 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN 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 411 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET 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 725 GLN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 939 GLN 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 1029 VAL Chi-restraints excluded: chain A residue 1049 MET 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 157 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 66 GLN A 164 ASN A 189 GLN A 486 GLN A1084 HIS B 63 HIS B 429 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.082905 restraints weight = 18526.106| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.64 r_work: 0.2706 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13903 Z= 0.144 Angle : 0.513 9.821 18842 Z= 0.269 Chirality : 0.042 0.168 2101 Planarity : 0.004 0.044 2400 Dihedral : 6.166 85.988 1940 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.61 % Allowed : 15.47 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1684 helix: 0.58 (0.19), residues: 810 sheet: -0.93 (0.37), residues: 156 loop : -0.69 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 606 HIS 0.006 0.001 HIS A1036 PHE 0.016 0.001 PHE A 206 TYR 0.018 0.001 TYR B 13 ARG 0.005 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 571) hydrogen bonds : angle 4.51627 ( 1650) covalent geometry : bond 0.00347 (13903) covalent geometry : angle 0.51253 (18842) *********************** 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 275 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: A 20 ARG cc_start: 0.8851 (mtm180) cc_final: 0.8618 (mtm180) REVERT: A 319 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 479 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7880 (mmm160) REVERT: A 532 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9083 (mtt) REVERT: A 706 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8472 (mt-10) REVERT: A 725 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: A 809 SER cc_start: 0.8977 (t) cc_final: 0.8665 (p) REVERT: A 922 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8337 (ttpt) REVERT: A 939 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8482 (tp40) REVERT: A 957 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8684 (ptmm) REVERT: A 978 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: A 1028 ASP cc_start: 0.8243 (t0) cc_final: 0.7822 (t0) REVERT: A 1173 GLN cc_start: 0.7137 (mt0) cc_final: 0.6633 (mm-40) REVERT: B 43 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 136 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7005 (mttp) REVERT: B 404 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8405 (m-30) REVERT: B 413 ASP cc_start: 0.8484 (p0) cc_final: 0.8264 (p0) REVERT: B 443 ARG cc_start: 0.6186 (mpt180) cc_final: 0.5486 (mtt180) REVERT: B 452 MET cc_start: 0.9288 (tpt) cc_final: 0.9069 (tpt) outliers start: 68 outliers final: 32 residues processed: 245 average time/residue: 1.5869 time to fit residues: 421.0210 Evaluate side-chains 235 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 131 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 462 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 589 VAL 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 720 ILE Chi-restraints excluded: chain A residue 725 GLN 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 841 ARG Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 939 GLN 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 1029 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 118 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 887 GLN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.083891 restraints weight = 18803.474| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.65 r_work: 0.2677 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13903 Z= 0.117 Angle : 0.483 10.148 18842 Z= 0.254 Chirality : 0.040 0.176 2101 Planarity : 0.004 0.056 2400 Dihedral : 5.925 79.391 1940 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.00 % Allowed : 16.82 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1684 helix: 0.84 (0.19), residues: 807 sheet: -0.94 (0.37), residues: 163 loop : -0.54 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 606 HIS 0.005 0.001 HIS A1036 PHE 0.014 0.001 PHE A 206 TYR 0.014 0.001 TYR A1183 ARG 0.008 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 571) hydrogen bonds : angle 4.41986 ( 1650) covalent geometry : bond 0.00279 (13903) covalent geometry : angle 0.48283 (18842) *********************** 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 265 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8857 (mtm180) cc_final: 0.8635 (mtm180) REVERT: A 319 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8162 (mm) REVERT: A 479 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7821 (mmm160) REVERT: A 706 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8434 (mt-10) REVERT: A 725 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: A 809 SER cc_start: 0.8919 (t) cc_final: 0.8613 (p) REVERT: A 978 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: A 1028 ASP cc_start: 0.8237 (t0) cc_final: 0.7770 (t0) REVERT: A 1173 GLN cc_start: 0.7053 (mt0) cc_final: 0.6649 (mm-40) REVERT: B 11 LYS cc_start: 0.9094 (mptp) cc_final: 0.8800 (mmtm) REVERT: B 43 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 413 ASP cc_start: 0.8410 (p0) cc_final: 0.7850 (t0) REVERT: B 443 ARG cc_start: 0.6171 (mpt180) cc_final: 0.5229 (mpt180) REVERT: B 452 MET cc_start: 0.9258 (tpt) cc_final: 0.9032 (tpt) outliers start: 59 outliers final: 32 residues processed: 241 average time/residue: 1.5182 time to fit residues: 395.8325 Evaluate side-chains 237 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 199 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 483 ASP Chi-restraints excluded: chain A residue 545 SER 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 712 THR Chi-restraints excluded: chain A residue 725 GLN 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 841 ARG 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 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 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 340 VAL Chi-restraints excluded: chain B residue 348 THR 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 75 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 887 GLN A1084 HIS B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.082094 restraints weight = 18892.358| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.64 r_work: 0.2655 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3949 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= 0.163 Angle : 0.519 9.986 18842 Z= 0.273 Chirality : 0.042 0.203 2101 Planarity : 0.004 0.040 2400 Dihedral : 5.846 73.996 1940 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 16.35 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1684 helix: 0.92 (0.19), residues: 806 sheet: -0.89 (0.37), residues: 163 loop : -0.45 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 606 HIS 0.005 0.001 HIS A 413 PHE 0.016 0.001 PHE A 206 TYR 0.015 0.001 TYR A1183 ARG 0.004 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 571) hydrogen bonds : angle 4.46248 ( 1650) covalent geometry : bond 0.00397 (13903) covalent geometry : angle 0.51943 (18842) *********************** 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 268 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: A 37 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (ttp80) REVERT: A 319 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7124 (mm) REVERT: A 320 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7883 (mtm-85) REVERT: A 375 ASN cc_start: 0.8100 (t0) cc_final: 0.7869 (t0) REVERT: A 479 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7759 (mtp180) REVERT: A 706 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8452 (mt-10) REVERT: A 809 SER cc_start: 0.8962 (t) cc_final: 0.8663 (p) REVERT: A 922 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8214 (ttpt) REVERT: A 978 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: A 1028 ASP cc_start: 0.8315 (t0) cc_final: 0.7802 (t0) REVERT: B 11 LYS cc_start: 0.9106 (mptp) cc_final: 0.8820 (mmtm) REVERT: B 43 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7837 (mp) REVERT: B 413 ASP cc_start: 0.8464 (p0) cc_final: 0.7908 (t0) REVERT: B 443 ARG cc_start: 0.6341 (mpt180) cc_final: 0.5398 (mpt180) outliers start: 67 outliers final: 40 residues processed: 237 average time/residue: 1.5239 time to fit residues: 389.4060 Evaluate side-chains 239 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 131 LYS 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 320 ARG Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP 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 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 841 ARG 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 978 GLN Chi-restraints excluded: chain A residue 996 SER 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 235 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 322 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.082142 restraints weight = 18679.280| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 1.69 r_work: 0.2650 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4055 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= 0.152 Angle : 0.509 10.199 18842 Z= 0.267 Chirality : 0.042 0.207 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.704 68.485 1940 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.14 % Allowed : 16.82 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1684 helix: 1.00 (0.19), residues: 806 sheet: -0.81 (0.37), residues: 163 loop : -0.39 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 606 HIS 0.005 0.001 HIS A1036 PHE 0.016 0.001 PHE A 206 TYR 0.015 0.001 TYR A1183 ARG 0.004 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 571) hydrogen bonds : angle 4.45093 ( 1650) covalent geometry : bond 0.00369 (13903) covalent geometry : angle 0.50940 (18842) *********************** 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 257 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: A 37 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8360 (ttp80) REVERT: A 131 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8572 (ttmt) REVERT: A 319 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8250 (mm) REVERT: A 375 ASN cc_start: 0.8119 (t0) cc_final: 0.7844 (t0) REVERT: A 479 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7631 (mtp180) REVERT: A 706 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8416 (mt-10) REVERT: A 809 SER cc_start: 0.8986 (t) cc_final: 0.8650 (p) REVERT: A 922 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8274 (ttpt) REVERT: A 974 GLN cc_start: 0.7421 (tt0) cc_final: 0.7219 (tt0) REVERT: A 978 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: A 1028 ASP cc_start: 0.8354 (t0) cc_final: 0.7804 (t0) REVERT: B 11 LYS cc_start: 0.9083 (mptp) cc_final: 0.8807 (mmtm) REVERT: B 43 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7846 (mp) REVERT: B 136 LYS cc_start: 0.7269 (mmtm) cc_final: 0.6922 (mttp) REVERT: B 413 ASP cc_start: 0.8441 (p0) cc_final: 0.7951 (t0) REVERT: B 443 ARG cc_start: 0.6333 (mpt180) cc_final: 0.5431 (mpt180) outliers start: 61 outliers final: 41 residues processed: 234 average time/residue: 1.5358 time to fit residues: 387.7838 Evaluate side-chains 240 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 131 LYS 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 287 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP 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 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 854 ASP 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 978 GLN Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1026 VAL 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 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 427 ILE 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 138 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- 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** A 887 GLN 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 = 0.3059 r_free = 0.3059 target = 0.101600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.083508 restraints weight = 18706.104| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.63 r_work: 0.2690 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13903 Z= 0.121 Angle : 0.490 10.294 18842 Z= 0.255 Chirality : 0.040 0.215 2101 Planarity : 0.003 0.039 2400 Dihedral : 5.492 63.981 1940 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.87 % Allowed : 17.50 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1684 helix: 1.14 (0.19), residues: 806 sheet: -0.42 (0.41), residues: 133 loop : -0.34 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 606 HIS 0.005 0.001 HIS A1036 PHE 0.014 0.001 PHE A 206 TYR 0.014 0.001 TYR A1183 ARG 0.007 0.000 ARG A 950 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 571) hydrogen bonds : angle 4.37024 ( 1650) covalent geometry : bond 0.00291 (13903) covalent geometry : angle 0.48977 (18842) *********************** 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 252 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8393 (ttp80) REVERT: A 131 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8590 (ttmt) REVERT: A 199 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8699 (m) REVERT: A 319 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 479 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7719 (mtp180) REVERT: A 492 LEU cc_start: 0.9038 (mp) cc_final: 0.8715 (mp) REVERT: A 706 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8423 (mt-10) REVERT: A 809 SER cc_start: 0.8956 (t) cc_final: 0.8676 (p) REVERT: A 922 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8329 (ttpt) REVERT: A 978 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6865 (mp10) REVERT: A 1014 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8132 (ptp) REVERT: A 1028 ASP cc_start: 0.8324 (t0) cc_final: 0.7797 (t0) REVERT: B 11 LYS cc_start: 0.9100 (mptp) cc_final: 0.8788 (mmtm) REVERT: B 43 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7814 (mp) REVERT: B 136 LYS cc_start: 0.7295 (mmtm) cc_final: 0.6825 (mttp) REVERT: B 204 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8447 (mtt-85) REVERT: B 413 ASP cc_start: 0.8405 (p0) cc_final: 0.7994 (t0) REVERT: B 443 ARG cc_start: 0.6374 (mpt180) cc_final: 0.5449 (mpt180) REVERT: B 502 ASP cc_start: 0.8131 (t0) cc_final: 0.7862 (t0) outliers start: 57 outliers final: 35 residues processed: 225 average time/residue: 1.5129 time to fit residues: 368.5835 Evaluate side-chains 232 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 131 LYS 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 320 ARG Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP 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 712 THR 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 854 ASP 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 978 GLN Chi-restraints excluded: chain A residue 996 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A 939 GLN B 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.099866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.081485 restraints weight = 18667.168| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.68 r_work: 0.2643 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13903 Z= 0.165 Angle : 0.534 9.891 18842 Z= 0.277 Chirality : 0.042 0.218 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.500 61.012 1940 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.73 % Allowed : 18.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1684 helix: 1.11 (0.19), residues: 807 sheet: -0.41 (0.40), residues: 141 loop : -0.41 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 606 HIS 0.005 0.001 HIS A 413 PHE 0.016 0.001 PHE A 206 TYR 0.015 0.001 TYR A1183 ARG 0.006 0.000 ARG A 950 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 571) hydrogen bonds : angle 4.43719 ( 1650) covalent geometry : bond 0.00403 (13903) covalent geometry : angle 0.53388 (18842) *********************** 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 254 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: A 131 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8558 (ttmt) REVERT: A 319 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 375 ASN cc_start: 0.8079 (t0) cc_final: 0.7873 (t0) REVERT: A 479 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7435 (mtp180) REVERT: A 706 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8398 (mt-10) REVERT: A 809 SER cc_start: 0.8993 (t) cc_final: 0.8665 (p) REVERT: A 922 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8271 (ttpt) REVERT: A 978 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: A 1014 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8152 (ptp) REVERT: A 1028 ASP cc_start: 0.8354 (t0) cc_final: 0.7828 (t0) REVERT: B 11 LYS cc_start: 0.9090 (mptp) cc_final: 0.8807 (mmtm) REVERT: B 43 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 44 ARG cc_start: 0.8390 (mtm110) cc_final: 0.8169 (mtm180) REVERT: B 136 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6856 (mttp) REVERT: B 162 GLU cc_start: 0.8301 (tt0) cc_final: 0.8066 (tt0) REVERT: B 413 ASP cc_start: 0.8352 (p0) cc_final: 0.7962 (t0) REVERT: B 443 ARG cc_start: 0.6360 (mpt180) cc_final: 0.5472 (mpt180) REVERT: B 502 ASP cc_start: 0.8153 (t0) cc_final: 0.7924 (t0) outliers start: 55 outliers final: 36 residues processed: 231 average time/residue: 1.5694 time to fit residues: 390.5897 Evaluate side-chains 235 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 131 LYS 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 287 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP 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 712 THR 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 854 ASP 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 954 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 996 SER 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 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 21 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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** A 887 GLN 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 = 0.3021 r_free = 0.3021 target = 0.099189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.081017 restraints weight = 18847.659| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.62 r_work: 0.2632 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13903 Z= 0.176 Angle : 0.555 10.968 18842 Z= 0.287 Chirality : 0.043 0.214 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.485 58.125 1940 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.46 % Allowed : 18.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1684 helix: 1.10 (0.19), residues: 807 sheet: -0.40 (0.40), residues: 141 loop : -0.42 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 606 HIS 0.006 0.001 HIS A1036 PHE 0.017 0.001 PHE A 206 TYR 0.016 0.001 TYR A1183 ARG 0.006 0.000 ARG A 950 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 571) hydrogen bonds : angle 4.47264 ( 1650) covalent geometry : bond 0.00430 (13903) covalent geometry : angle 0.55480 (18842) ********************** 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 247 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: A 131 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8609 (ttmt) REVERT: A 199 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8699 (m) REVERT: A 319 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 479 ARG cc_start: 0.8165 (mtp180) cc_final: 0.7547 (mtp180) REVERT: A 706 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8471 (mt-10) REVERT: A 809 SER cc_start: 0.8926 (t) cc_final: 0.8624 (p) REVERT: A 922 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8345 (ttpt) REVERT: A 951 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8287 (ttm170) REVERT: A 957 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8769 (ptmm) REVERT: A 978 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: A 1014 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8147 (ptp) REVERT: A 1028 ASP cc_start: 0.8290 (t0) cc_final: 0.7764 (t0) REVERT: B 11 LYS cc_start: 0.9108 (mptp) cc_final: 0.8842 (mmtm) REVERT: B 43 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 136 LYS cc_start: 0.7409 (mmtm) cc_final: 0.7059 (mttp) REVERT: B 413 ASP cc_start: 0.8378 (p0) cc_final: 0.8026 (t0) REVERT: B 443 ARG cc_start: 0.6487 (mpt180) cc_final: 0.5604 (mpt180) REVERT: B 502 ASP cc_start: 0.8138 (t0) cc_final: 0.7920 (t0) outliers start: 51 outliers final: 36 residues processed: 225 average time/residue: 1.5378 time to fit residues: 372.9315 Evaluate side-chains 235 residues out of total 1475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 131 LYS 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 287 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 483 ASP 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 712 THR 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 854 ASP Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR 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 996 SER Chi-restraints excluded: chain A residue 1014 MET Chi-restraints excluded: chain A residue 1026 VAL 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 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 165 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** A 669 ASN A 887 GLN B 63 HIS B 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.098011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.079782 restraints weight = 18868.497| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.62 r_work: 0.2608 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13903 Z= 0.227 Angle : 0.595 10.296 18842 Z= 0.309 Chirality : 0.044 0.233 2101 Planarity : 0.004 0.039 2400 Dihedral : 5.565 55.895 1940 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.46 % Allowed : 18.66 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1684 helix: 0.99 (0.19), residues: 806 sheet: -0.44 (0.40), residues: 141 loop : -0.47 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 606 HIS 0.007 0.001 HIS A1036 PHE 0.019 0.002 PHE A 206 TYR 0.018 0.002 TYR A1183 ARG 0.006 0.001 ARG A 950 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 571) hydrogen bonds : angle 4.58412 ( 1650) covalent geometry : bond 0.00556 (13903) covalent geometry : angle 0.59521 (18842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11351.92 seconds wall clock time: 198 minutes 35.54 seconds (11915.54 seconds total)