Starting phenix.real_space_refine on Sat Sep 12 12:16:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tz2_20587/09_2026/6tz2_20587.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 96 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 9573 2.51 5 N 2628 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9667 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 38, 'TRANS': 1169} Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4007 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 482} Chain breaks: 2 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 15} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "N" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'RNAv2': 36} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 31} Link IDs: {'rna2p': 5, 'rna3p': 30} Chain: "T" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 792 Classifications: {'RNAv2': 36} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 34} Link IDs: {'rna2p': 2, 'rna3p': 33} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.82, per 1000 atoms: 0.18 Number of scatterers: 15608 At special positions: 0 Unit cell: (119.68, 145.52, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 96 15.00 Mg 2 11.99 O 3255 8.00 N 2628 7.00 C 9573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 482.9 milliseconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 16 sheets defined 51.3% alpha, 8.3% beta 21 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.597A pdb=" N ASN A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 19 through 36 removed outlier: 4.023A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.641A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.152A pdb=" N THR A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.705A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.585A 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 Processing helix chain 'A' and resid 165 through 175 removed outlier: 4.053A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.294A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.742A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.756A pdb=" N LYS A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.658A pdb=" N ALA A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 removed outlier: 3.531A pdb=" N SER A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.594A pdb=" N LEU A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 324 through 340 removed outlier: 3.970A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 3.859A pdb=" N SER A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 410 removed outlier: 3.787A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 431 through 438 removed outlier: 3.813A pdb=" N LYS A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 457 through 460 removed outlier: 3.773A pdb=" N TYR A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.099A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.599A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.641A pdb=" N TYR A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 removed outlier: 4.139A pdb=" N LEU A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 537 removed outlier: 3.838A pdb=" N SER A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.949A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.606A pdb=" N GLN A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 666 removed outlier: 3.773A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.540A pdb=" N THR A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.594A pdb=" N ALA A 756 " --> pdb=" O ARG A 752 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.787A 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: 3.585A pdb=" N MET A 839 " --> pdb=" O TRP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 879 removed outlier: 4.381A pdb=" N LEU A 874 " --> pdb=" O TYR A 870 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 901 through 912 removed outlier: 3.922A pdb=" N ALA A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 938 removed outlier: 3.590A pdb=" N GLU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 959 removed outlier: 3.835A pdb=" N SER A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 985 removed outlier: 3.504A pdb=" N ALA A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'A' and resid 1016 through 1020 removed outlier: 4.056A pdb=" N LEU A1019 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 removed outlier: 3.977A pdb=" N HIS A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1062 Processing helix chain 'A' and resid 1075 through 1081 removed outlier: 4.238A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1102 removed outlier: 3.578A pdb=" N SER A1102 " --> pdb=" O LYS A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1105 No H-bonds generated for 'chain 'A' and resid 1103 through 1105' Processing helix chain 'A' and resid 1106 through 1115 Processing helix chain 'A' and resid 1117 through 1133 removed outlier: 3.752A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.504A pdb=" N ALA A1158 " --> pdb=" O PRO A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1189 removed outlier: 3.550A pdb=" N LEU A1177 " --> pdb=" O GLN A1173 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1212 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.517A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.531A pdb=" N MET B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.222A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.591A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.594A pdb=" N LEU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 removed outlier: 4.324A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.233A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.541A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 441 through 457 removed outlier: 3.545A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.632A pdb=" N PHE B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.699A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 Processing helix chain 'B' and resid 524 through 538 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.776A pdb=" N TRP B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.675A pdb=" N TYR A 55 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.852A 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: 3.620A 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: 6.491A pdb=" N MET A 373 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN A 383 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 371 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 476 through 478 Processing sheet with id=AA6, first strand: chain 'A' and resid 672 through 677 removed outlier: 5.529A pdb=" N LEU A 672 " --> pdb=" O GLN A 687 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 687 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR A 674 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 685 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 714 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 621 through 622 Processing sheet with id=AA8, first strand: chain 'A' and resid 720 through 722 removed outlier: 4.047A pdb=" N LEU A 726 " --> pdb=" O TRP A 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 791 through 792 Processing sheet with id=AB1, first strand: chain 'A' and resid 867 through 868 Processing sheet with id=AB2, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.682A pdb=" N GLU A1023 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.770A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AB6, first strand: chain 'B' and resid 266 through 267 removed outlier: 4.075A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR B 261 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE B 313 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.941A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 347 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL B 487 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 348 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 543 " --> pdb=" O THR B 504 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2353 1.30 - 1.43: 4828 1.43 - 1.55: 8648 1.55 - 1.68: 190 1.68 - 1.81: 97 Bond restraints: 16116 Sorted by residual: bond pdb=" C2' ATP A1301 " pdb=" C3' ATP A1301 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C3' UTP A1302 " pdb=" C4' UTP A1302 " ideal model delta sigma weight residual 1.527 1.296 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" O5' ATP A1301 " pdb=" PA ATP A1301 " ideal model delta sigma weight residual 1.579 1.704 -0.125 1.10e-02 8.26e+03 1.30e+02 bond pdb=" C1' ATP A1301 " pdb=" C2' ATP A1301 " ideal model delta sigma weight residual 1.531 1.657 -0.126 1.20e-02 6.94e+03 1.10e+02 bond pdb=" C1' UTP A1302 " pdb=" C2' UTP A1302 " ideal model delta sigma weight residual 1.525 1.326 0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 16111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 22066 4.12 - 8.25: 159 8.25 - 12.37: 14 12.37 - 16.49: 2 16.49 - 20.62: 4 Bond angle restraints: 22245 Sorted by residual: angle pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 123.59 142.43 -18.84 1.08e+00 8.64e-01 3.07e+02 angle pdb=" N1 ATP A1301 " pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 118.11 97.49 20.62 1.23e+00 6.64e-01 2.82e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 123.37 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 123.36 13.47 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C1' ATP A1301 " pdb=" N9 ATP A1301 " pdb=" C4 ATP A1301 " ideal model delta sigma weight residual 126.88 108.64 18.24 1.80e+00 3.09e-01 1.03e+02 ... (remaining 22240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 8651 15.38 - 30.76: 517 30.76 - 46.14: 215 46.14 - 61.51: 86 61.51 - 76.89: 23 Dihedral angle restraints: 9492 sinusoidal: 4460 harmonic: 5032 Sorted by residual: dihedral pdb=" C4' U N 25 " pdb=" C3' U N 25 " pdb=" C2' U N 25 " pdb=" C1' U N 25 " ideal model delta sinusoidal sigma weight residual 36.34 -39.37 75.72 1 3.10e+00 1.04e-01 7.53e+02 dihedral pdb=" C4' U N 19 " pdb=" C3' U N 19 " pdb=" C2' U N 19 " pdb=" C1' U N 19 " ideal model delta sinusoidal sigma weight residual 36.34 -37.79 74.14 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' U N 24 " pdb=" C3' U N 24 " pdb=" C2' U N 24 " pdb=" C1' U N 24 " ideal model delta sinusoidal sigma weight residual 36.34 -37.48 73.82 1 3.10e+00 1.04e-01 7.21e+02 ... (remaining 9489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1963 0.063 - 0.125: 425 0.125 - 0.188: 54 0.188 - 0.251: 92 0.251 - 0.313: 36 Chirality restraints: 2570 Sorted by residual: chirality pdb=" C3' U N 25 " pdb=" C4' U N 25 " pdb=" O3' U N 25 " pdb=" C2' U N 25 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE A 881 " pdb=" CA ILE A 881 " pdb=" CG1 ILE A 881 " pdb=" CG2 ILE A 881 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" P U N 17 " pdb=" OP1 U N 17 " pdb=" OP2 U N 17 " pdb=" O5' U N 17 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2567 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.028 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 606 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 996 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C SER A 996 " 0.050 2.00e-02 2.50e+03 pdb=" O SER A 996 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 997 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 538 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.69e+00 pdb=" N PRO B 539 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 539 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 539 " 0.035 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 202 2.64 - 3.20: 13482 3.20 - 3.77: 24302 3.77 - 4.33: 32900 4.33 - 4.90: 52419 Nonbonded interactions: 123305 Sorted by model distance: nonbonded pdb=" O2A UTP A1302 " pdb="MG MG A1303 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1303 " model vdw 2.095 2.170 nonbonded pdb=" O3A UTP A1302 " pdb="MG MG A1304 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASP A 681 " pdb="MG MG A1303 " model vdw 2.112 2.170 nonbonded pdb=" O3G UTP A1302 " pdb="MG MG A1304 " model vdw 2.156 2.170 ... (remaining 123300 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.009 0.289 16116 Z= 0.452 Angle : 1.031 20.615 22245 Z= 0.557 Chirality : 0.073 0.313 2570 Planarity : 0.007 0.065 2510 Dihedral : 13.295 76.891 6258 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.47 % Allowed : 5.17 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.16), residues: 1701 helix: -2.42 (0.14), residues: 764 sheet: -1.85 (0.39), residues: 150 loop : -2.29 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 336 TYR 0.027 0.003 TYR B 286 PHE 0.034 0.003 PHE A 769 TRP 0.064 0.004 TRP A 606 HIS 0.013 0.002 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.45 (16116) covalent geometry : angle 1.03099 / 0.56 (22245) hydrogen bonds : bond 0.17836 / 11.43 ( 597) hydrogen bonds : angle 7.00157 / 4.86 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 506 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7870 (tp40) cc_final: 0.7644 (mm-40) REVERT: A 374 SER cc_start: 0.8558 (t) cc_final: 0.8295 (p) REVERT: A 415 GLU cc_start: 0.8084 (tp30) cc_final: 0.7580 (tp30) REVERT: A 421 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8105 (tm) REVERT: A 514 ASN cc_start: 0.7599 (t160) cc_final: 0.7011 (p0) REVERT: A 595 ARG cc_start: 0.7392 (ttt90) cc_final: 0.6901 (mmt-90) REVERT: A 630 VAL cc_start: 0.9464 (t) cc_final: 0.9128 (m) REVERT: A 643 ASP cc_start: 0.8541 (p0) cc_final: 0.8030 (p0) REVERT: A 794 LEU cc_start: 0.8339 (tp) cc_final: 0.7958 (tt) REVERT: A 839 MET cc_start: 0.8991 (mmp) cc_final: 0.8710 (mmm) REVERT: A 877 ASP cc_start: 0.8104 (t0) cc_final: 0.7873 (t70) REVERT: A 910 ASP cc_start: 0.8856 (t0) cc_final: 0.8236 (t0) REVERT: A 911 LEU cc_start: 0.9238 (mt) cc_final: 0.8976 (mt) REVERT: A 912 ASN cc_start: 0.8765 (m-40) cc_final: 0.8530 (t0) REVERT: A 942 LYS cc_start: 0.9198 (mmpt) cc_final: 0.8584 (mmtm) REVERT: A 978 GLN cc_start: 0.9230 (tt0) cc_final: 0.9002 (tt0) REVERT: A 1022 TYR cc_start: 0.8341 (p90) cc_final: 0.7666 (p90) REVERT: A 1074 LEU cc_start: 0.8134 (tt) cc_final: 0.7930 (tt) REVERT: B 85 THR cc_start: 0.8954 (m) cc_final: 0.8735 (p) REVERT: B 132 ILE cc_start: 0.9067 (mt) cc_final: 0.8778 (mp) REVERT: B 284 ASP cc_start: 0.8220 (m-30) cc_final: 0.8007 (m-30) REVERT: B 384 ASP cc_start: 0.8806 (p0) cc_final: 0.8575 (p0) REVERT: B 416 SER cc_start: 0.9257 (t) cc_final: 0.8962 (p) REVERT: B 420 GLN cc_start: 0.8145 (mt0) cc_final: 0.7668 (mt0) REVERT: B 433 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 436 GLN cc_start: 0.8507 (mt0) cc_final: 0.8082 (mt0) REVERT: B 464 ASP cc_start: 0.7915 (m-30) cc_final: 0.7618 (m-30) outliers start: 7 outliers final: 2 residues processed: 512 average time/residue: 0.1275 time to fit residues: 93.9050 Evaluate side-chains 323 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 ASN A 691 ASN A 694 HIS A 696 HIS A 700 ASN A 820 ASN A 888 ASN A 939 GLN A1020 HIS A1140 HIS B 165 GLN B 180 GLN B 182 HIS B 272 ASN B 414 ASN B 542 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101644 restraints weight = 27289.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104060 restraints weight = 13357.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105648 restraints weight = 8415.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106613 restraints weight = 6331.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107202 restraints weight = 5391.096| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16116 Z= 0.140 Angle : 0.781 15.155 22245 Z= 0.345 Chirality : 0.060 0.767 2570 Planarity : 0.005 0.054 2510 Dihedral : 13.170 151.155 3013 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 11.96 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.19), residues: 1701 helix: -0.63 (0.17), residues: 780 sheet: -1.66 (0.40), residues: 145 loop : -1.69 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 487 TYR 0.030 0.001 TYR A1134 PHE 0.021 0.001 PHE A 783 TRP 0.024 0.002 TRP A 606 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16116) covalent geometry : angle 0.78058 / 0.34 (22245) hydrogen bonds : bond 0.04921 / 3.21 ( 597) hydrogen bonds : angle 4.95243 / 3.43 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7899 (tp40) cc_final: 0.7598 (mm-40) REVERT: A 415 GLU cc_start: 0.8354 (tp30) cc_final: 0.7808 (tp30) REVERT: A 432 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8064 (mp0) REVERT: A 483 ASP cc_start: 0.8762 (t70) cc_final: 0.8353 (t0) REVERT: A 595 ARG cc_start: 0.7255 (ttt90) cc_final: 0.6889 (mmt-90) REVERT: A 643 ASP cc_start: 0.8624 (p0) cc_final: 0.8201 (p0) REVERT: A 752 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7445 (mtp85) REVERT: A 794 LEU cc_start: 0.8205 (tp) cc_final: 0.7756 (tt) REVERT: A 844 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 877 ASP cc_start: 0.8013 (t0) cc_final: 0.7757 (t70) REVERT: A 910 ASP cc_start: 0.8807 (t0) cc_final: 0.8569 (t0) REVERT: A 986 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7706 (pt0) REVERT: A 997 ARG cc_start: 0.8216 (mmt180) cc_final: 0.7818 (mmm-85) REVERT: A 1022 TYR cc_start: 0.8670 (p90) cc_final: 0.7769 (p90) REVERT: A 1066 ASP cc_start: 0.6038 (t0) cc_final: 0.5768 (t0) REVERT: A 1130 TYR cc_start: 0.8527 (t80) cc_final: 0.8276 (t80) REVERT: A 1134 TYR cc_start: 0.7767 (p90) cc_final: 0.7433 (p90) REVERT: B 85 THR cc_start: 0.8964 (m) cc_final: 0.8760 (p) REVERT: B 207 GLU cc_start: 0.7324 (tt0) cc_final: 0.7055 (pm20) REVERT: B 359 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7916 (ptpt) REVERT: B 419 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 433 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8159 (mm-30) REVERT: B 454 GLU cc_start: 0.8094 (tp30) cc_final: 0.7636 (tt0) REVERT: B 464 ASP cc_start: 0.7962 (m-30) cc_final: 0.7706 (m-30) outliers start: 44 outliers final: 31 residues processed: 385 average time/residue: 0.1194 time to fit residues: 67.1086 Evaluate side-chains 324 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 171 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 176 optimal weight: 50.0000 chunk 114 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 978 GLN ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 63 HIS B 180 GLN B 420 GLN B 453 ASN B 492 ASN B 542 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097721 restraints weight = 27715.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100094 restraints weight = 13763.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101674 restraints weight = 8807.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102622 restraints weight = 6705.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103088 restraints weight = 5741.859| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16116 Z= 0.235 Angle : 0.726 11.186 22245 Z= 0.338 Chirality : 0.055 0.596 2570 Planarity : 0.005 0.044 2510 Dihedral : 13.181 160.970 3013 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 4.77 % Allowed : 13.10 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1701 helix: 0.21 (0.18), residues: 775 sheet: -1.38 (0.41), residues: 150 loop : -1.38 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 20 TYR 0.025 0.002 TYR A1134 PHE 0.019 0.002 PHE A 769 TRP 0.026 0.002 TRP A 606 HIS 0.005 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (16116) covalent geometry : angle 0.72638 / 0.34 (22245) hydrogen bonds : bond 0.05164 / 3.37 ( 597) hydrogen bonds : angle 4.84046 / 3.38 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 302 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.9405 (mtpp) cc_final: 0.9084 (mtpt) REVERT: A 345 LEU cc_start: 0.9076 (mt) cc_final: 0.8789 (mt) REVERT: A 415 GLU cc_start: 0.8391 (tp30) cc_final: 0.7878 (tp30) REVERT: A 421 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8691 (tp) REVERT: A 483 ASP cc_start: 0.8737 (t70) cc_final: 0.8289 (t0) REVERT: A 595 ARG cc_start: 0.7601 (ttt90) cc_final: 0.7373 (tpp-160) REVERT: A 643 ASP cc_start: 0.8585 (p0) cc_final: 0.8217 (p0) REVERT: A 752 ARG cc_start: 0.7683 (mtp85) cc_final: 0.7476 (mtp85) REVERT: A 844 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 887 GLN cc_start: 0.8400 (pm20) cc_final: 0.8094 (pm20) REVERT: A 986 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7688 (pt0) REVERT: A 997 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7954 (mtm180) REVERT: A 1045 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 1191 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8822 (t) REVERT: B 359 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7817 (ptpt) outliers start: 71 outliers final: 49 residues processed: 341 average time/residue: 0.1239 time to fit residues: 61.7845 Evaluate side-chains 328 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 545 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 92 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 chunk 63 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 126 HIS B 180 GLN B 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099590 restraints weight = 27768.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102025 restraints weight = 13888.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103629 restraints weight = 8916.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104604 restraints weight = 6810.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105130 restraints weight = 5840.937| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16116 Z= 0.139 Angle : 0.651 11.287 22245 Z= 0.297 Chirality : 0.052 0.604 2570 Planarity : 0.004 0.042 2510 Dihedral : 12.945 159.701 3013 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.30 % Allowed : 15.19 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1701 helix: 0.65 (0.19), residues: 783 sheet: -1.14 (0.41), residues: 153 loop : -1.24 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 266 TYR 0.029 0.001 TYR A1134 PHE 0.015 0.001 PHE A1110 TRP 0.016 0.001 TRP A 445 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16116) covalent geometry : angle 0.65090 / 0.30 (22245) hydrogen bonds : bond 0.04187 / 2.75 ( 597) hydrogen bonds : angle 4.47895 / 3.12 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8466 (ttmt) REVERT: A 179 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8149 (t0) REVERT: A 189 GLN cc_start: 0.6887 (tp-100) cc_final: 0.6262 (mm-40) REVERT: A 415 GLU cc_start: 0.8357 (tp30) cc_final: 0.7860 (tp30) REVERT: A 421 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8569 (tp) REVERT: A 434 GLU cc_start: 0.8559 (mp0) cc_final: 0.8114 (mp0) REVERT: A 483 ASP cc_start: 0.8734 (t70) cc_final: 0.8162 (t0) REVERT: A 643 ASP cc_start: 0.8583 (p0) cc_final: 0.8197 (p0) REVERT: A 794 LEU cc_start: 0.8355 (tp) cc_final: 0.8009 (tt) REVERT: A 844 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 887 GLN cc_start: 0.8297 (pm20) cc_final: 0.7969 (pm20) REVERT: A 971 TYR cc_start: 0.8072 (m-10) cc_final: 0.7758 (m-10) REVERT: A 986 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7743 (pt0) REVERT: A 997 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7974 (mmm-85) REVERT: A 1066 ASP cc_start: 0.5960 (t0) cc_final: 0.5745 (t0) REVERT: A 1191 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8627 (t) REVERT: B 322 MET cc_start: 0.8365 (mtp) cc_final: 0.8118 (mtt) REVERT: B 359 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7936 (ptpt) REVERT: B 366 TYR cc_start: 0.9152 (t80) cc_final: 0.8722 (t80) REVERT: B 416 SER cc_start: 0.8602 (t) cc_final: 0.8067 (p) REVERT: B 464 ASP cc_start: 0.7879 (m-30) cc_final: 0.7474 (m-30) outliers start: 64 outliers final: 44 residues processed: 345 average time/residue: 0.1283 time to fit residues: 64.3545 Evaluate side-chains 330 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 30 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 116 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 413 HIS B 492 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100885 restraints weight = 27457.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103300 restraints weight = 13674.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104898 restraints weight = 8755.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105892 restraints weight = 6662.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106327 restraints weight = 5692.373| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16116 Z= 0.121 Angle : 0.620 10.735 22245 Z= 0.283 Chirality : 0.050 0.500 2570 Planarity : 0.004 0.041 2510 Dihedral : 12.793 159.335 3013 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.77 % Allowed : 15.73 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1701 helix: 0.89 (0.19), residues: 789 sheet: -1.08 (0.40), residues: 163 loop : -1.18 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 266 TYR 0.009 0.001 TYR A1134 PHE 0.014 0.001 PHE A1110 TRP 0.017 0.001 TRP A 445 HIS 0.004 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16116) covalent geometry : angle 0.61974 / 0.28 (22245) hydrogen bonds : bond 0.03887 / 2.58 ( 597) hydrogen bonds : angle 4.33362 / 3.03 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8466 (ttmt) REVERT: A 179 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (t0) REVERT: A 189 GLN cc_start: 0.7279 (tp-100) cc_final: 0.6949 (mm-40) REVERT: A 415 GLU cc_start: 0.8254 (tp30) cc_final: 0.7882 (tp30) REVERT: A 421 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 483 ASP cc_start: 0.8755 (t70) cc_final: 0.8097 (t0) REVERT: A 643 ASP cc_start: 0.8551 (p0) cc_final: 0.8194 (p0) REVERT: A 696 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8695 (t-90) REVERT: A 745 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6410 (tm-30) REVERT: A 794 LEU cc_start: 0.8374 (tp) cc_final: 0.8075 (tt) REVERT: A 844 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 854 ASP cc_start: 0.7642 (p0) cc_final: 0.7376 (p0) REVERT: A 887 GLN cc_start: 0.8367 (pm20) cc_final: 0.8098 (pm20) REVERT: A 959 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7711 (tpt-90) REVERT: A 971 TYR cc_start: 0.8290 (m-10) cc_final: 0.7920 (m-10) REVERT: A 986 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7822 (pt0) REVERT: A 997 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7935 (mmm-85) REVERT: A 1014 MET cc_start: 0.8669 (ttp) cc_final: 0.8184 (tmm) REVERT: A 1066 ASP cc_start: 0.5952 (t0) cc_final: 0.5695 (t0) REVERT: A 1134 TYR cc_start: 0.7780 (p90) cc_final: 0.7511 (p90) REVERT: A 1156 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9148 (m) REVERT: B 359 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (ptpt) REVERT: B 366 TYR cc_start: 0.9185 (t80) cc_final: 0.8825 (t80) REVERT: B 464 ASP cc_start: 0.7802 (m-30) cc_final: 0.7401 (m-30) REVERT: B 477 THR cc_start: 0.9227 (p) cc_final: 0.9003 (t) outliers start: 71 outliers final: 49 residues processed: 346 average time/residue: 0.1178 time to fit residues: 60.3198 Evaluate side-chains 332 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 696 HIS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 80 optimal weight: 20.0000 chunk 170 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 HIS B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098311 restraints weight = 27403.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100640 restraints weight = 13884.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102146 restraints weight = 8984.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103117 restraints weight = 6890.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103556 restraints weight = 5928.131| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16116 Z= 0.191 Angle : 0.665 9.582 22245 Z= 0.308 Chirality : 0.051 0.437 2570 Planarity : 0.004 0.039 2510 Dihedral : 12.809 160.009 3011 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.91 % Allowed : 16.33 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1701 helix: 1.01 (0.19), residues: 782 sheet: -1.20 (0.40), residues: 151 loop : -1.08 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 266 TYR 0.027 0.001 TYR A1100 PHE 0.016 0.001 PHE A1110 TRP 0.017 0.001 TRP A 445 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (16116) covalent geometry : angle 0.66530 / 0.31 (22245) hydrogen bonds : bond 0.04432 / 2.93 ( 597) hydrogen bonds : angle 4.50867 / 3.16 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 286 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8523 (ttmt) REVERT: A 179 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (t0) REVERT: A 189 GLN cc_start: 0.7654 (tp-100) cc_final: 0.7371 (mm-40) REVERT: A 415 GLU cc_start: 0.8301 (tp30) cc_final: 0.7928 (tp30) REVERT: A 421 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8774 (tp) REVERT: A 483 ASP cc_start: 0.8833 (t70) cc_final: 0.8107 (t0) REVERT: A 643 ASP cc_start: 0.8653 (p0) cc_final: 0.8322 (p0) REVERT: A 844 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 854 ASP cc_start: 0.7687 (p0) cc_final: 0.7425 (p0) REVERT: A 971 TYR cc_start: 0.8322 (m-10) cc_final: 0.7853 (m-10) REVERT: A 986 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7854 (pt0) REVERT: A 997 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8033 (mmm-85) REVERT: A 1134 TYR cc_start: 0.7902 (p90) cc_final: 0.7619 (p90) REVERT: A 1156 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9173 (m) REVERT: B 322 MET cc_start: 0.8385 (mtp) cc_final: 0.8019 (mtt) REVERT: B 359 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7907 (ptpt) REVERT: B 366 TYR cc_start: 0.9178 (t80) cc_final: 0.8763 (t80) REVERT: B 416 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8102 (p) REVERT: B 464 ASP cc_start: 0.7848 (m-30) cc_final: 0.7505 (m-30) outliers start: 73 outliers final: 58 residues processed: 324 average time/residue: 0.1218 time to fit residues: 58.5890 Evaluate side-chains 340 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 0.0470 chunk 166 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 0.0670 chunk 114 optimal weight: 10.0000 overall best weight: 3.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100263 restraints weight = 27220.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102608 restraints weight = 13769.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104168 restraints weight = 8907.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105016 restraints weight = 6837.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105639 restraints weight = 5917.485| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16116 Z= 0.126 Angle : 0.629 10.462 22245 Z= 0.287 Chirality : 0.049 0.389 2570 Planarity : 0.004 0.039 2510 Dihedral : 12.695 159.289 3011 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.64 % Allowed : 17.20 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1701 helix: 1.08 (0.19), residues: 789 sheet: -1.10 (0.39), residues: 161 loop : -1.05 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 266 TYR 0.022 0.001 TYR A1100 PHE 0.013 0.001 PHE A1110 TRP 0.015 0.001 TRP A 445 HIS 0.006 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16116) covalent geometry : angle 0.62917 / 0.29 (22245) hydrogen bonds : bond 0.03845 / 2.55 ( 597) hydrogen bonds : angle 4.31561 / 3.03 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 289 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8471 (ttmt) REVERT: A 179 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 189 GLN cc_start: 0.7525 (tp-100) cc_final: 0.7262 (mm-40) REVERT: A 415 GLU cc_start: 0.8317 (tp30) cc_final: 0.7944 (tp30) REVERT: A 421 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8738 (tp) REVERT: A 483 ASP cc_start: 0.8764 (t70) cc_final: 0.8146 (t0) REVERT: A 643 ASP cc_start: 0.8581 (p0) cc_final: 0.8265 (p0) REVERT: A 794 LEU cc_start: 0.8214 (tp) cc_final: 0.7896 (tt) REVERT: A 844 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 854 ASP cc_start: 0.7690 (p0) cc_final: 0.7445 (p0) REVERT: A 971 TYR cc_start: 0.8327 (m-10) cc_final: 0.7815 (m-10) REVERT: A 986 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7926 (pt0) REVERT: A 997 ARG cc_start: 0.8306 (mmt180) cc_final: 0.8007 (mmm-85) REVERT: A 1134 TYR cc_start: 0.7807 (p90) cc_final: 0.7530 (p90) REVERT: A 1156 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9155 (m) REVERT: B 322 MET cc_start: 0.8375 (mtp) cc_final: 0.8039 (mtt) REVERT: B 359 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7946 (ptpt) REVERT: B 366 TYR cc_start: 0.9174 (t80) cc_final: 0.8841 (t80) REVERT: B 416 SER cc_start: 0.8481 (t) cc_final: 0.7856 (p) REVERT: B 464 ASP cc_start: 0.7827 (m-30) cc_final: 0.7424 (m-30) outliers start: 69 outliers final: 54 residues processed: 328 average time/residue: 0.1206 time to fit residues: 58.5539 Evaluate side-chains 342 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 28 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 78 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 HIS B 9 HIS B 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101791 restraints weight = 27487.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104204 restraints weight = 13806.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105786 restraints weight = 8872.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106798 restraints weight = 6765.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107274 restraints weight = 5791.134| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16116 Z= 0.106 Angle : 0.610 10.921 22245 Z= 0.277 Chirality : 0.049 0.323 2570 Planarity : 0.003 0.039 2510 Dihedral : 12.568 158.477 3011 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.23 % Allowed : 17.54 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1701 helix: 1.23 (0.19), residues: 794 sheet: -0.92 (0.39), residues: 162 loop : -1.04 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 266 TYR 0.021 0.001 TYR A1100 PHE 0.014 0.001 PHE A1110 TRP 0.016 0.001 TRP A 445 HIS 0.003 0.001 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16116) covalent geometry : angle 0.61015 / 0.28 (22245) hydrogen bonds : bond 0.03593 / 2.39 ( 597) hydrogen bonds : angle 4.18538 / 2.96 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 317 ARG cc_start: 0.8839 (ttt90) cc_final: 0.8553 (tmm-80) REVERT: A 415 GLU cc_start: 0.8291 (tp30) cc_final: 0.7948 (tp30) REVERT: A 421 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 480 GLN cc_start: 0.8390 (mt0) cc_final: 0.8077 (mt0) REVERT: A 483 ASP cc_start: 0.8717 (t70) cc_final: 0.8074 (t0) REVERT: A 643 ASP cc_start: 0.8568 (p0) cc_final: 0.8242 (p0) REVERT: A 696 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8657 (t-90) REVERT: A 745 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6644 (tm-30) REVERT: A 794 LEU cc_start: 0.8274 (tp) cc_final: 0.7948 (tt) REVERT: A 823 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.6022 (t80) REVERT: A 844 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 854 ASP cc_start: 0.7663 (p0) cc_final: 0.7419 (p0) REVERT: A 942 LYS cc_start: 0.8893 (mmpt) cc_final: 0.8448 (tppt) REVERT: A 971 TYR cc_start: 0.8301 (m-10) cc_final: 0.7778 (m-10) REVERT: A 993 ARG cc_start: 0.7508 (tpm170) cc_final: 0.7129 (tpp-160) REVERT: A 997 ARG cc_start: 0.8284 (mmt180) cc_final: 0.7978 (mmm-85) REVERT: A 1134 TYR cc_start: 0.7562 (p90) cc_final: 0.7196 (p90) REVERT: A 1156 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9146 (m) REVERT: A 1181 PHE cc_start: 0.9001 (m-10) cc_final: 0.8438 (m-80) REVERT: B 322 MET cc_start: 0.8213 (mtp) cc_final: 0.7849 (mtt) REVERT: B 343 ASN cc_start: 0.8385 (t0) cc_final: 0.8059 (t0) REVERT: B 366 TYR cc_start: 0.9162 (t80) cc_final: 0.8900 (t80) REVERT: B 414 ASN cc_start: 0.8530 (m-40) cc_final: 0.8328 (m-40) REVERT: B 454 GLU cc_start: 0.7871 (tp30) cc_final: 0.7508 (tp30) REVERT: B 464 ASP cc_start: 0.7833 (m-30) cc_final: 0.7519 (m-30) outliers start: 63 outliers final: 42 residues processed: 348 average time/residue: 0.1189 time to fit residues: 61.1402 Evaluate side-chains 336 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 696 HIS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 128 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 HIS B 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100686 restraints weight = 27549.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103082 restraints weight = 13964.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104645 restraints weight = 9031.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105638 restraints weight = 6920.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106110 restraints weight = 5933.695| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16116 Z= 0.131 Angle : 0.631 10.487 22245 Z= 0.288 Chirality : 0.049 0.321 2570 Planarity : 0.004 0.039 2510 Dihedral : 12.580 159.273 3011 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.17 % Allowed : 17.81 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1701 helix: 1.23 (0.19), residues: 791 sheet: -0.99 (0.39), residues: 161 loop : -0.95 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 266 TYR 0.024 0.001 TYR A 969 PHE 0.020 0.001 PHE A1110 TRP 0.014 0.001 TRP A 445 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16116) covalent geometry : angle 0.63148 / 0.29 (22245) hydrogen bonds : bond 0.03773 / 2.51 ( 597) hydrogen bonds : angle 4.25683 / 3.01 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8487 (ttpp) REVERT: A 317 ARG cc_start: 0.8890 (ttt90) cc_final: 0.8621 (tmm-80) REVERT: A 415 GLU cc_start: 0.8328 (tp30) cc_final: 0.7913 (tp30) REVERT: A 421 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 483 ASP cc_start: 0.8802 (t70) cc_final: 0.8002 (t0) REVERT: A 643 ASP cc_start: 0.8585 (p0) cc_final: 0.8265 (p0) REVERT: A 794 LEU cc_start: 0.8221 (tp) cc_final: 0.7901 (tt) REVERT: A 844 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 854 ASP cc_start: 0.7728 (p0) cc_final: 0.7458 (p0) REVERT: A 942 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8125 (mmmm) REVERT: A 971 TYR cc_start: 0.8280 (m-10) cc_final: 0.7782 (m-10) REVERT: A 993 ARG cc_start: 0.7527 (tpm170) cc_final: 0.7128 (tpp-160) REVERT: A 997 ARG cc_start: 0.8316 (mmt180) cc_final: 0.8026 (mmm-85) REVERT: A 1134 TYR cc_start: 0.7631 (p90) cc_final: 0.7251 (p90) REVERT: A 1156 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9165 (m) REVERT: A 1181 PHE cc_start: 0.9023 (m-10) cc_final: 0.8463 (m-80) REVERT: B 366 TYR cc_start: 0.9176 (t80) cc_final: 0.8905 (t80) REVERT: B 416 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 454 GLU cc_start: 0.7854 (tp30) cc_final: 0.7614 (tp30) REVERT: B 464 ASP cc_start: 0.7766 (m-30) cc_final: 0.7439 (m-30) outliers start: 62 outliers final: 51 residues processed: 328 average time/residue: 0.1199 time to fit residues: 58.3269 Evaluate side-chains 340 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1108 ASN B 63 HIS B 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099621 restraints weight = 27445.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101967 restraints weight = 13927.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103521 restraints weight = 9028.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104499 restraints weight = 6935.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104956 restraints weight = 5959.985| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16116 Z= 0.149 Angle : 0.649 9.522 22245 Z= 0.297 Chirality : 0.049 0.332 2570 Planarity : 0.004 0.038 2510 Dihedral : 12.624 161.516 3011 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.90 % Allowed : 17.94 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1701 helix: 1.23 (0.19), residues: 789 sheet: -0.93 (0.39), residues: 161 loop : -0.97 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 752 TYR 0.026 0.001 TYR A 969 PHE 0.018 0.001 PHE A1110 TRP 0.013 0.001 TRP A 445 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16116) covalent geometry : angle 0.64913 / 0.30 (22245) hydrogen bonds : bond 0.04013 / 2.67 ( 597) hydrogen bonds : angle 4.36395 / 3.09 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 415 GLU cc_start: 0.8345 (tp30) cc_final: 0.7923 (tp30) REVERT: A 421 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 483 ASP cc_start: 0.8750 (t70) cc_final: 0.8026 (t0) REVERT: A 643 ASP cc_start: 0.8590 (p0) cc_final: 0.8291 (p0) REVERT: A 794 LEU cc_start: 0.8389 (tp) cc_final: 0.7957 (tt) REVERT: A 844 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 854 ASP cc_start: 0.7706 (p0) cc_final: 0.7433 (p0) REVERT: A 942 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8128 (mmmm) REVERT: A 971 TYR cc_start: 0.8314 (m-10) cc_final: 0.7843 (m-10) REVERT: A 993 ARG cc_start: 0.7434 (tpm170) cc_final: 0.7070 (tpp-160) REVERT: A 1134 TYR cc_start: 0.7728 (p90) cc_final: 0.7377 (p90) REVERT: A 1156 VAL cc_start: 0.9459 (OUTLIER) cc_final: 0.9181 (m) REVERT: B 343 ASN cc_start: 0.8394 (t0) cc_final: 0.8064 (t0) REVERT: B 366 TYR cc_start: 0.9181 (t80) cc_final: 0.8843 (t80) REVERT: B 416 SER cc_start: 0.8648 (t) cc_final: 0.8046 (p) REVERT: B 454 GLU cc_start: 0.7937 (tp30) cc_final: 0.7684 (tp30) REVERT: B 464 ASP cc_start: 0.7778 (m-30) cc_final: 0.7414 (m-30) outliers start: 58 outliers final: 52 residues processed: 318 average time/residue: 0.1173 time to fit residues: 55.1790 Evaluate side-chains 334 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 280 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 961 HIS Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 538 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 156 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 8 optimal weight: 7.9990 chunk 140 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 413 HIS A 696 HIS B 63 HIS B 492 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106604 restraints weight = 27236.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109028 restraints weight = 13677.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110634 restraints weight = 8810.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111585 restraints weight = 6734.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112165 restraints weight = 5780.972| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16116 Z= 0.096 Angle : 0.621 11.406 22245 Z= 0.280 Chirality : 0.048 0.321 2570 Planarity : 0.003 0.040 2510 Dihedral : 12.413 162.249 3011 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.35 % Allowed : 20.03 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1701 helix: 1.32 (0.19), residues: 788 sheet: -0.39 (0.41), residues: 152 loop : -0.93 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 266 TYR 0.021 0.001 TYR A 969 PHE 0.018 0.001 PHE A1110 TRP 0.016 0.001 TRP A 445 HIS 0.005 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (16116) covalent geometry : angle 0.62089 / 0.28 (22245) hydrogen bonds : bond 0.03218 / 2.15 ( 597) hydrogen bonds : angle 4.10361 / 2.91 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.92 seconds wall clock time: 44 minutes 30.83 seconds (2670.83 seconds total)