Starting phenix.real_space_refine on Fri Jun 20 13:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7use_26734/06_2025/7use_26734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7use_26734/06_2025/7use_26734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7use_26734/06_2025/7use_26734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7use_26734/06_2025/7use_26734.map" model { file = "/net/cci-nas-00/data/ceres_data/7use_26734/06_2025/7use_26734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7use_26734/06_2025/7use_26734.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.056 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 6 5.49 5 Mg 2 5.21 5 S 161 5.16 5 C 15230 2.51 5 N 4067 2.21 5 O 4447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23913 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9602 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 43, 'TRANS': 1128} Chain breaks: 7 Chain: "B" Number of atoms: 8814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8814 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 38, 'TRANS': 1060} Chain breaks: 2 Chain: "C" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1386 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.20, per 1000 atoms: 0.55 Number of scatterers: 23913 At special positions: 0 Unit cell: (154.123, 149.745, 211.044, 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 161 16.00 P 6 15.00 Mg 2 11.99 O 4447 8.00 N 4067 7.00 C 15230 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: 5.55 Conformation dependent library (CDL) restraints added in 2.8 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 9 sheets defined 74.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.744A pdb=" N LEU A 17 " --> pdb=" O ASN A 13 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 85 removed outlier: 3.688A pdb=" N GLN A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 116 through 144 removed outlier: 3.528A pdb=" N THR A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 removed outlier: 4.259A pdb=" N LYS A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 removed outlier: 3.505A pdb=" N LEU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 230 removed outlier: 4.043A pdb=" N VAL A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.701A pdb=" N LEU A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 3.670A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 302 removed outlier: 4.361A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 4.179A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 4.468A pdb=" N GLU A 326 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 327 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 329 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 365 removed outlier: 3.774A pdb=" N ILE A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.569A pdb=" N TYR A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 444 through 468 Processing helix chain 'A' and resid 468 through 490 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'A' and resid 504 through 518 removed outlier: 3.585A pdb=" N VAL A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.665A pdb=" N ARG A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.851A pdb=" N ILE A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.504A pdb=" N SER A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.866A pdb=" N ILE A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.594A pdb=" N ASN A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.954A pdb=" N LEU A 621 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP A 622 " --> pdb=" O SER A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 622' Processing helix chain 'A' and resid 624 through 630 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 669 through 681 removed outlier: 3.564A pdb=" N ASP A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 723 removed outlier: 3.613A pdb=" N LEU A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.627A pdb=" N ARG A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 752 removed outlier: 4.643A pdb=" N LEU A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 789 removed outlier: 3.603A pdb=" N LEU A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 removed outlier: 6.183A pdb=" N THR A 793 " --> pdb=" O GLU A 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 794 through 814 Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 837 through 850 removed outlier: 3.555A pdb=" N LEU A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 903 removed outlier: 3.509A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 910 through 922 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 943 through 955 removed outlier: 3.513A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 955 " --> pdb=" O THR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 967 Processing helix chain 'A' and resid 968 through 980 removed outlier: 3.661A pdb=" N GLU A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 986 Processing helix chain 'A' and resid 987 through 991 Processing helix chain 'A' and resid 992 through 1025 removed outlier: 3.599A pdb=" N HIS A1024 " --> pdb=" O CYS A1020 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 removed outlier: 3.882A pdb=" N ASN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1055 through 1058 Processing helix chain 'A' and resid 1059 through 1066 Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1092 through 1104 Processing helix chain 'A' and resid 1106 through 1110 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.622A pdb=" N LEU A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1155 through 1168 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1200 through 1226 removed outlier: 3.652A pdb=" N MET A1204 " --> pdb=" O PRO A1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 12 through 40 removed outlier: 3.565A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.909A pdb=" N ILE B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.557A pdb=" N LYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.822A pdb=" N GLN B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 81' Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.551A pdb=" N ILE B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 118 Processing helix chain 'B' and resid 126 through 150 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.591A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.753A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.502A pdb=" N GLU B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 270 through 276 removed outlier: 4.220A pdb=" N ASN B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.575A pdb=" N SER B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 313 removed outlier: 4.314A pdb=" N ASN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 360 removed outlier: 5.481A pdb=" N GLY B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.822A pdb=" N GLY B 365 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 391 removed outlier: 3.502A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 removed outlier: 3.827A pdb=" N LEU B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 437 removed outlier: 3.752A pdb=" N MET B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 453 through 470 removed outlier: 3.676A pdb=" N ILE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.869A pdb=" N GLU B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 477' Processing helix chain 'B' and resid 483 through 499 removed outlier: 3.672A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 508 No H-bonds generated for 'chain 'B' and resid 506 through 508' Processing helix chain 'B' and resid 509 through 528 Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.565A pdb=" N PHE B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 Processing helix chain 'B' and resid 560 through 566 removed outlier: 4.015A pdb=" N ARG B 564 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 574 through 580 removed outlier: 4.078A pdb=" N MET B 577 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 580 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 627 removed outlier: 4.495A pdb=" N HIS B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 removed outlier: 6.116A pdb=" N LYS B 631 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 673 through 692 removed outlier: 3.578A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 724 removed outlier: 3.934A pdb=" N TYR B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 724 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 755 Processing helix chain 'B' and resid 761 through 774 Processing helix chain 'B' and resid 783 through 796 Processing helix chain 'B' and resid 796 through 803 Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 844 through 872 removed outlier: 3.587A pdb=" N LYS B 868 " --> pdb=" O ALA B 864 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 882 removed outlier: 3.791A pdb=" N THR B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.525A pdb=" N MET B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 930 removed outlier: 4.116A pdb=" N VAL B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 904 " --> pdb=" O VAL B 900 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.504A pdb=" N ALA B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 988 through 1007 removed outlier: 3.729A pdb=" N MET B1000 " --> pdb=" O ALA B 996 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B1001 " --> pdb=" O CYS B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1017 removed outlier: 5.822A pdb=" N VAL B1014 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET B1015 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B1017 " --> pdb=" O VAL B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1047 Processing helix chain 'B' and resid 1051 through 1072 removed outlier: 4.046A pdb=" N GLU B1072 " --> pdb=" O LYS B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.631A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1107 removed outlier: 3.559A pdb=" N LEU B1103 " --> pdb=" O THR B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1121 removed outlier: 4.220A pdb=" N LEU B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 81 removed outlier: 4.066A pdb=" N ILE C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 83 No H-bonds generated for 'chain 'C' and resid 82 through 83' Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 128 removed outlier: 4.129A pdb=" N CYS C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'D' and resid 11 through 69 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 11 through 40 Processing helix chain 'E' and resid 42 through 111 removed outlier: 4.057A pdb=" N ALA E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 61 through 66 removed outlier: 4.553A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 96 removed outlier: 3.565A pdb=" N PHE F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.519A pdb=" N HIS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.978A pdb=" N ASP F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.643A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 3.857A pdb=" N PHE F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 Processing helix chain 'G' and resid 68 through 72 Processing helix chain 'G' and resid 86 through 96 removed outlier: 3.566A pdb=" N PHE G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG G 94 " --> pdb=" O PHE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.567A pdb=" N ILE G 126 " --> pdb=" O ASP G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.642A pdb=" N GLY G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 removed outlier: 3.817A pdb=" N VAL G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 306 Processing sheet with id=AA2, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.579A pdb=" N VAL A 755 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 855 through 858 Processing sheet with id=AA4, first strand: chain 'A' and resid 1090 through 1091 Processing sheet with id=AA5, first strand: chain 'B' and resid 292 through 296 removed outlier: 6.929A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 695 through 697 Processing sheet with id=AA7, first strand: chain 'B' and resid 805 through 808 removed outlier: 3.537A pdb=" N ALA B 806 " --> pdb=" O VAL B 815 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 46 removed outlier: 6.072A pdb=" N ILE F 4 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TRP F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE F 78 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS F 153 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 37 through 46 removed outlier: 3.544A pdb=" N ASP G 38 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR G 58 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY G 10 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 7 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE G 78 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL G 113 " --> pdb=" O PHE G 78 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 80 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR G 115 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE G 82 " --> pdb=" O THR G 115 " (cutoff:3.500A) 1539 hydrogen bonds defined for protein. 4467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.51 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3961 1.32 - 1.44: 6305 1.44 - 1.56: 13850 1.56 - 1.69: 10 1.69 - 1.81: 256 Bond restraints: 24382 Sorted by residual: bond pdb=" N3B GNP F 500 " pdb=" PG GNP F 500 " ideal model delta sigma weight residual 1.801 1.633 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" CA ARG A 196 " pdb=" C ARG A 196 " ideal model delta sigma weight residual 1.532 1.476 0.056 9.60e-03 1.09e+04 3.44e+01 bond pdb=" N ILE F 33 " pdb=" CA ILE F 33 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.70e-03 1.69e+04 1.99e+01 bond pdb=" N VAL A 105 " pdb=" CA VAL A 105 " ideal model delta sigma weight residual 1.461 1.410 0.051 1.19e-02 7.06e+03 1.83e+01 bond pdb=" O3A GNP F 500 " pdb=" PB GNP F 500 " ideal model delta sigma weight residual 1.687 1.607 0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 24377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 32325 2.96 - 5.91: 613 5.91 - 8.87: 26 8.87 - 11.83: 7 11.83 - 14.78: 2 Bond angle restraints: 32973 Sorted by residual: angle pdb=" N ARG A 196 " pdb=" CA ARG A 196 " pdb=" C ARG A 196 " ideal model delta sigma weight residual 110.91 101.76 9.15 1.17e+00 7.31e-01 6.11e+01 angle pdb=" CA GLU F 127 " pdb=" C GLU F 127 " pdb=" O GLU F 127 " ideal model delta sigma weight residual 120.90 114.18 6.72 1.03e+00 9.43e-01 4.26e+01 angle pdb=" N THR G 35 " pdb=" CA THR G 35 " pdb=" C THR G 35 " ideal model delta sigma weight residual 108.02 118.56 -10.54 1.75e+00 3.27e-01 3.63e+01 angle pdb=" N LYS F 123 " pdb=" CA LYS F 123 " pdb=" C LYS F 123 " ideal model delta sigma weight residual 111.71 104.88 6.83 1.15e+00 7.56e-01 3.52e+01 angle pdb=" CA GLY A 968 " pdb=" C GLY A 968 " pdb=" O GLY A 968 " ideal model delta sigma weight residual 122.29 117.68 4.61 8.10e-01 1.52e+00 3.24e+01 ... (remaining 32968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 14686 35.89 - 71.78: 200 71.78 - 107.68: 19 107.68 - 143.57: 0 143.57 - 179.46: 3 Dihedral angle restraints: 14908 sinusoidal: 6153 harmonic: 8755 Sorted by residual: dihedral pdb=" C5' GTP G 500 " pdb=" O5' GTP G 500 " pdb=" PA GTP G 500 " pdb=" O3A GTP G 500 " ideal model delta sinusoidal sigma weight residual 69.27 -110.19 179.46 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP G 500 " pdb=" O3A GTP G 500 " pdb=" PB GTP G 500 " pdb=" PA GTP G 500 " ideal model delta sinusoidal sigma weight residual 291.08 139.08 152.00 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C8 GTP G 500 " pdb=" C1' GTP G 500 " pdb=" N9 GTP G 500 " pdb=" O4' GTP G 500 " ideal model delta sinusoidal sigma weight residual 104.59 -46.36 150.95 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 14905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3191 0.063 - 0.126: 447 0.126 - 0.188: 76 0.188 - 0.251: 19 0.251 - 0.314: 5 Chirality restraints: 3738 Sorted by residual: chirality pdb=" CA ILE F 110 " pdb=" N ILE F 110 " pdb=" C ILE F 110 " pdb=" CB ILE F 110 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE B 463 " pdb=" N PHE B 463 " pdb=" C PHE B 463 " pdb=" CB PHE B 463 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR A 108 " pdb=" N TYR A 108 " pdb=" C TYR A 108 " pdb=" CB TYR A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3735 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 58 " 0.027 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C ARG A 58 " -0.096 2.00e-02 2.50e+03 pdb=" O ARG A 58 " 0.037 2.00e-02 2.50e+03 pdb=" N TYR A 59 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 149 " -0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C ARG A 149 " 0.074 2.00e-02 2.50e+03 pdb=" O ARG A 149 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS A 150 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 721 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C VAL B 721 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL B 721 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 722 " -0.021 2.00e-02 2.50e+03 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 51 2.45 - 3.06: 16369 3.06 - 3.68: 35899 3.68 - 4.29: 51089 4.29 - 4.90: 86865 Nonbonded interactions: 190273 Sorted by model distance: nonbonded pdb=" CG2 THR G 35 " pdb="MG MG G 501 " model vdw 1.840 2.590 nonbonded pdb=" O3G GTP G 500 " pdb="MG MG G 501 " model vdw 2.072 2.170 nonbonded pdb=" O PHE F 37 " pdb=" OD1 ASP F 38 " model vdw 2.163 3.040 nonbonded pdb=" NH1 ARG B 611 " pdb=" OD1 ASN B 612 " model vdw 2.184 3.120 nonbonded pdb=" O1B GTP G 500 " pdb="MG MG G 501 " model vdw 2.198 2.170 ... (remaining 190268 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 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 2 through 60 or resid 62 through 177 or resid 501)) selection = (chain 'G' and (resid 2 through 60 or resid 62 through 177 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 51.410 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 0.005 0.168 24382 Z= 0.357 Angle : 0.795 14.784 32973 Z= 0.553 Chirality : 0.047 0.314 3738 Planarity : 0.004 0.056 4188 Dihedral : 13.677 179.459 9210 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.19 % Allowed : 1.05 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.16), residues: 2920 helix: 3.18 (0.12), residues: 1949 sheet: 2.38 (0.56), residues: 90 loop : 0.01 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 56 HIS 0.009 0.001 HIS A 889 PHE 0.023 0.001 PHE A 975 TYR 0.016 0.001 TYR A1138 ARG 0.007 0.000 ARG B 297 Details of bonding type rmsd hydrogen bonds : bond 0.18339 ( 1539) hydrogen bonds : angle 5.54468 ( 4467) covalent geometry : bond 0.00497 (24382) covalent geometry : angle 0.79488 (32973) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 673 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6747 (mm-30) REVERT: A 566 LEU cc_start: 0.8515 (tp) cc_final: 0.8314 (tm) REVERT: A 704 TYR cc_start: 0.7314 (t80) cc_final: 0.7110 (t80) REVERT: A 1204 MET cc_start: 0.7104 (ttt) cc_final: 0.6824 (ttt) REVERT: B 94 TYR cc_start: 0.7596 (t80) cc_final: 0.7361 (t80) REVERT: B 254 SER cc_start: 0.8319 (t) cc_final: 0.7164 (t) REVERT: B 691 TYR cc_start: 0.8121 (t80) cc_final: 0.7196 (t80) REVERT: C 70 GLN cc_start: 0.8455 (tp40) cc_final: 0.8214 (tp40) REVERT: F 23 TYR cc_start: 0.8703 (t80) cc_final: 0.8420 (t80) REVERT: F 119 LEU cc_start: 0.8248 (mt) cc_final: 0.7726 (mm) REVERT: F 155 LEU cc_start: 0.8007 (mt) cc_final: 0.7728 (mp) REVERT: F 165 LEU cc_start: 0.7997 (tp) cc_final: 0.7787 (tt) REVERT: G 26 ASN cc_start: 0.8063 (t0) cc_final: 0.7784 (t0) REVERT: G 45 MET cc_start: 0.6437 (mtt) cc_final: 0.6231 (mtm) REVERT: G 63 ASP cc_start: 0.6759 (p0) cc_final: 0.6399 (p0) outliers start: 5 outliers final: 5 residues processed: 677 average time/residue: 1.5918 time to fit residues: 1210.6998 Evaluate side-chains 542 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 537 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain F residue 124 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 149 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 208 GLN A 473 ASN A 596 HIS A 614 GLN A1030 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 448 ASN B 555 GLN B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.115455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104669 restraints weight = 48574.502| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.69 r_work: 0.3428 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24382 Z= 0.162 Angle : 0.635 10.619 32973 Z= 0.329 Chirality : 0.042 0.157 3738 Planarity : 0.004 0.046 4188 Dihedral : 6.536 150.964 3280 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.36 % Allowed : 12.84 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.16), residues: 2920 helix: 2.72 (0.12), residues: 1953 sheet: 1.59 (0.50), residues: 109 loop : 0.08 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 97 HIS 0.007 0.001 HIS B1117 PHE 0.018 0.001 PHE A 600 TYR 0.029 0.001 TYR B 140 ARG 0.009 0.001 ARG E 84 Details of bonding type rmsd hydrogen bonds : bond 0.05587 ( 1539) hydrogen bonds : angle 4.10304 ( 4467) covalent geometry : bond 0.00362 (24382) covalent geometry : angle 0.63535 (32973) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 537 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8334 (mmm) cc_final: 0.7809 (mmm) REVERT: A 74 GLU cc_start: 0.8266 (pp20) cc_final: 0.7310 (pp20) REVERT: A 75 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 78 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7524 (pp20) REVERT: A 206 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 275 ASP cc_start: 0.7969 (m-30) cc_final: 0.7695 (m-30) REVERT: A 310 ASP cc_start: 0.8457 (t0) cc_final: 0.8076 (t0) REVERT: A 354 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8216 (mt-10) REVERT: A 357 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7696 (ttp) REVERT: A 446 GLU cc_start: 0.8217 (mp0) cc_final: 0.7847 (pm20) REVERT: A 447 GLU cc_start: 0.7759 (mp0) cc_final: 0.7247 (mp0) REVERT: A 546 LYS cc_start: 0.8106 (pptt) cc_final: 0.7808 (pptt) REVERT: A 598 GLU cc_start: 0.7784 (tp30) cc_final: 0.7398 (tp30) REVERT: A 614 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8251 (pp30) REVERT: A 751 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8715 (mtmp) REVERT: A 763 ASP cc_start: 0.7863 (t0) cc_final: 0.7618 (t70) REVERT: A 807 MET cc_start: 0.8586 (tpp) cc_final: 0.8207 (ttp) REVERT: A 964 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7669 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7960 (pp20) REVERT: A 1051 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7866 (pp20) REVERT: A 1084 GLU cc_start: 0.7687 (pp20) cc_final: 0.7294 (pp20) REVERT: A 1134 MET cc_start: 0.8224 (mtt) cc_final: 0.8010 (mtt) REVERT: A 1163 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8228 (ttp) REVERT: A 1178 ASP cc_start: 0.7431 (t0) cc_final: 0.6981 (t0) REVERT: A 1216 ASP cc_start: 0.8407 (p0) cc_final: 0.8106 (p0) REVERT: B 135 ASP cc_start: 0.8381 (m-30) cc_final: 0.8112 (m-30) REVERT: B 211 GLN cc_start: 0.7728 (tp40) cc_final: 0.7459 (tp-100) REVERT: B 228 GLN cc_start: 0.8874 (mt0) cc_final: 0.7996 (mt0) REVERT: B 351 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8433 (ttmm) REVERT: B 407 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7350 (mm-30) REVERT: B 413 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 421 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8531 (ttpp) REVERT: B 479 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 558 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 725 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8713 (mtm) REVERT: B 826 ASN cc_start: 0.8847 (m110) cc_final: 0.8579 (m110) REVERT: B 828 GLU cc_start: 0.8395 (pm20) cc_final: 0.8066 (pm20) REVERT: B 886 LYS cc_start: 0.8130 (mppt) cc_final: 0.7859 (mppt) REVERT: B 926 ASP cc_start: 0.7727 (p0) cc_final: 0.7440 (p0) REVERT: B 1121 LYS cc_start: 0.8468 (pttm) cc_final: 0.8159 (pptt) REVERT: C 71 GLU cc_start: 0.8216 (tp30) cc_final: 0.7930 (tp30) REVERT: D 62 GLU cc_start: 0.8426 (tp30) cc_final: 0.7990 (tp30) REVERT: E 39 GLN cc_start: 0.8504 (pp30) cc_final: 0.8293 (tm-30) REVERT: F 53 LEU cc_start: 0.8422 (tp) cc_final: 0.8192 (pp) REVERT: F 118 ASP cc_start: 0.7851 (p0) cc_final: 0.7591 (p0) REVERT: F 119 LEU cc_start: 0.8505 (mt) cc_final: 0.8065 (mm) REVERT: F 122 ASP cc_start: 0.6652 (m-30) cc_final: 0.6401 (m-30) REVERT: F 124 ASP cc_start: 0.5235 (t70) cc_final: 0.5034 (t0) REVERT: F 154 TYR cc_start: 0.8227 (t80) cc_final: 0.7984 (t80) REVERT: G 44 VAL cc_start: 0.8817 (p) cc_final: 0.8601 (m) REVERT: G 63 ASP cc_start: 0.7704 (p0) cc_final: 0.7376 (p0) REVERT: G 105 CYS cc_start: 0.7396 (m) cc_final: 0.7178 (m) REVERT: G 156 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6822 (mm-30) REVERT: G 174 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8361 (ttm110) outliers start: 63 outliers final: 18 residues processed: 561 average time/residue: 1.6487 time to fit residues: 1039.4425 Evaluate side-chains 522 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 498 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 6 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 249 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 262 optimal weight: 40.0000 chunk 166 optimal weight: 8.9990 chunk 99 optimal weight: 0.0670 chunk 232 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 0.0870 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 243 ASN A 596 HIS ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.114626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103756 restraints weight = 48690.731| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.69 r_work: 0.3416 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24382 Z= 0.138 Angle : 0.588 10.363 32973 Z= 0.302 Chirality : 0.039 0.160 3738 Planarity : 0.004 0.048 4188 Dihedral : 6.281 148.662 3273 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.52 % Allowed : 15.69 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.16), residues: 2920 helix: 2.60 (0.12), residues: 1950 sheet: 1.53 (0.50), residues: 109 loop : 0.04 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 97 HIS 0.012 0.001 HIS A1058 PHE 0.016 0.001 PHE A 600 TYR 0.024 0.001 TYR B 140 ARG 0.010 0.001 ARG A 597 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 1539) hydrogen bonds : angle 3.89957 ( 4467) covalent geometry : bond 0.00304 (24382) covalent geometry : angle 0.58839 (32973) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 523 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8383 (mmm) cc_final: 0.7883 (mmm) REVERT: A 72 MET cc_start: 0.8484 (ttm) cc_final: 0.8240 (ttm) REVERT: A 74 GLU cc_start: 0.8286 (pp20) cc_final: 0.7332 (pp20) REVERT: A 75 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 78 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: A 114 VAL cc_start: 0.8957 (t) cc_final: 0.8642 (p) REVERT: A 166 ASN cc_start: 0.7501 (t0) cc_final: 0.7239 (t0) REVERT: A 206 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 212 MET cc_start: 0.8777 (mmp) cc_final: 0.8448 (mmt) REVERT: A 310 ASP cc_start: 0.8548 (t0) cc_final: 0.7972 (t0) REVERT: A 446 GLU cc_start: 0.8244 (mp0) cc_final: 0.7813 (pm20) REVERT: A 447 GLU cc_start: 0.7747 (mp0) cc_final: 0.7336 (mp0) REVERT: A 598 GLU cc_start: 0.7897 (tp30) cc_final: 0.7499 (tp30) REVERT: A 614 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: A 631 THR cc_start: 0.8773 (m) cc_final: 0.8433 (t) REVERT: A 747 GLU cc_start: 0.8069 (mp0) cc_final: 0.7735 (mp0) REVERT: A 751 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8695 (mtmm) REVERT: A 763 ASP cc_start: 0.7907 (t0) cc_final: 0.7525 (t0) REVERT: A 807 MET cc_start: 0.8671 (tpp) cc_final: 0.8248 (ttp) REVERT: A 878 ASP cc_start: 0.8148 (t0) cc_final: 0.7863 (t0) REVERT: A 953 MET cc_start: 0.9064 (mmm) cc_final: 0.8838 (tpp) REVERT: A 961 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8205 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8033 (pp20) REVERT: A 1043 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7855 (tm) REVERT: A 1051 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7875 (pp20) REVERT: A 1084 GLU cc_start: 0.7735 (pp20) cc_final: 0.7255 (pp20) REVERT: A 1092 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7235 (ptm) REVERT: A 1163 MET cc_start: 0.8432 (ptm) cc_final: 0.8205 (ttp) REVERT: A 1178 ASP cc_start: 0.7572 (t0) cc_final: 0.7136 (t0) REVERT: A 1193 ASP cc_start: 0.7912 (t70) cc_final: 0.7557 (t0) REVERT: A 1216 ASP cc_start: 0.8423 (p0) cc_final: 0.8211 (p0) REVERT: B 51 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7587 (mmmt) REVERT: B 78 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7444 (tm-30) REVERT: B 122 ASP cc_start: 0.8014 (t0) cc_final: 0.7412 (t0) REVERT: B 135 ASP cc_start: 0.8421 (m-30) cc_final: 0.8199 (m-30) REVERT: B 151 GLU cc_start: 0.7557 (tp30) cc_final: 0.7186 (tm-30) REVERT: B 207 LEU cc_start: 0.8348 (mt) cc_final: 0.8119 (mm) REVERT: B 211 GLN cc_start: 0.7866 (tp40) cc_final: 0.7526 (tp-100) REVERT: B 392 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: B 407 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7476 (mm-30) REVERT: B 479 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 510 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6089 (mtp85) REVERT: B 531 GLU cc_start: 0.8196 (mp0) cc_final: 0.7956 (mp0) REVERT: B 558 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 725 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: B 727 ASN cc_start: 0.7902 (t0) cc_final: 0.7691 (t0) REVERT: B 826 ASN cc_start: 0.8862 (m110) cc_final: 0.8594 (m110) REVERT: B 828 GLU cc_start: 0.8384 (pm20) cc_final: 0.8129 (pm20) REVERT: B 886 LYS cc_start: 0.8252 (mppt) cc_final: 0.7818 (mppt) REVERT: C 71 GLU cc_start: 0.8266 (tp30) cc_final: 0.7893 (tp30) REVERT: D 62 GLU cc_start: 0.8447 (tp30) cc_final: 0.8013 (tp30) REVERT: E 39 GLN cc_start: 0.8513 (pp30) cc_final: 0.8267 (tm-30) REVERT: F 57 ASP cc_start: 0.7847 (t0) cc_final: 0.7273 (t0) REVERT: F 119 LEU cc_start: 0.8531 (mt) cc_final: 0.8170 (mm) REVERT: F 122 ASP cc_start: 0.6642 (m-30) cc_final: 0.6217 (m-30) REVERT: F 165 LEU cc_start: 0.8834 (tp) cc_final: 0.8613 (mm) REVERT: G 44 VAL cc_start: 0.8820 (p) cc_final: 0.8615 (m) REVERT: G 63 ASP cc_start: 0.7839 (p0) cc_final: 0.7552 (p0) REVERT: G 122 ASP cc_start: 0.5965 (t0) cc_final: 0.5732 (t0) REVERT: G 145 MET cc_start: 0.8307 (tpp) cc_final: 0.8084 (tpp) REVERT: G 156 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7031 (mm-30) REVERT: G 174 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8452 (ttm110) outliers start: 67 outliers final: 20 residues processed: 549 average time/residue: 1.6646 time to fit residues: 1027.6339 Evaluate side-chains 531 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 504 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 55 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 275 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS A 596 HIS ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 418 HIS B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091017 restraints weight = 49778.671| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.69 r_work: 0.3361 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24382 Z= 0.172 Angle : 0.622 11.055 32973 Z= 0.317 Chirality : 0.041 0.167 3738 Planarity : 0.004 0.051 4188 Dihedral : 6.257 149.188 3273 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.36 % Allowed : 17.72 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.16), residues: 2920 helix: 2.48 (0.12), residues: 1952 sheet: 1.35 (0.48), residues: 109 loop : -0.11 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 97 HIS 0.005 0.001 HIS B1117 PHE 0.014 0.001 PHE F 37 TYR 0.026 0.001 TYR B 930 ARG 0.010 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 1539) hydrogen bonds : angle 3.87001 ( 4467) covalent geometry : bond 0.00396 (24382) covalent geometry : angle 0.62237 (32973) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 514 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8430 (mmm) cc_final: 0.7934 (mmm) REVERT: A 72 MET cc_start: 0.8527 (ttm) cc_final: 0.8261 (ttm) REVERT: A 74 GLU cc_start: 0.8317 (pp20) cc_final: 0.7361 (pp20) REVERT: A 75 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 78 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: A 114 VAL cc_start: 0.8928 (t) cc_final: 0.8575 (p) REVERT: A 262 MET cc_start: 0.7958 (tmm) cc_final: 0.7686 (tmm) REVERT: A 310 ASP cc_start: 0.8550 (t0) cc_final: 0.7904 (t0) REVERT: A 351 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 381 GLN cc_start: 0.8017 (mp10) cc_final: 0.7465 (mp10) REVERT: A 446 GLU cc_start: 0.8362 (mp0) cc_final: 0.7935 (pm20) REVERT: A 447 GLU cc_start: 0.7920 (mp0) cc_final: 0.7588 (mp0) REVERT: A 546 LYS cc_start: 0.8111 (pptt) cc_final: 0.7821 (pptt) REVERT: A 598 GLU cc_start: 0.7983 (tp30) cc_final: 0.7606 (tp30) REVERT: A 614 GLN cc_start: 0.8650 (tt0) cc_final: 0.8270 (tm-30) REVERT: A 631 THR cc_start: 0.8727 (m) cc_final: 0.8342 (t) REVERT: A 730 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8306 (tp30) REVERT: A 747 GLU cc_start: 0.8142 (mp0) cc_final: 0.7836 (mp0) REVERT: A 763 ASP cc_start: 0.8014 (t0) cc_final: 0.7788 (t70) REVERT: A 807 MET cc_start: 0.8742 (tpp) cc_final: 0.8295 (ttp) REVERT: A 878 ASP cc_start: 0.8242 (t0) cc_final: 0.7950 (t0) REVERT: A 961 ARG cc_start: 0.8462 (mtt90) cc_final: 0.8239 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8080 (pp20) REVERT: A 1043 LEU cc_start: 0.8209 (tt) cc_final: 0.7914 (tm) REVERT: A 1084 GLU cc_start: 0.7803 (pp20) cc_final: 0.7327 (pp20) REVERT: A 1092 MET cc_start: 0.7358 (ptm) cc_final: 0.7088 (ptm) REVERT: A 1163 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: A 1178 ASP cc_start: 0.7743 (t0) cc_final: 0.7273 (t0) REVERT: A 1193 ASP cc_start: 0.7949 (t70) cc_final: 0.7595 (t0) REVERT: A 1216 ASP cc_start: 0.8432 (p0) cc_final: 0.8208 (p0) REVERT: B 51 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7637 (mmmt) REVERT: B 78 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7468 (tm-30) REVERT: B 122 ASP cc_start: 0.8057 (t0) cc_final: 0.7477 (t0) REVERT: B 151 GLU cc_start: 0.7583 (tp30) cc_final: 0.7225 (tm-30) REVERT: B 211 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7616 (tp-100) REVERT: B 352 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7963 (tp30) REVERT: B 413 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 479 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 510 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6144 (mtp85) REVERT: B 531 GLU cc_start: 0.8283 (mp0) cc_final: 0.7920 (mp0) REVERT: B 725 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8302 (mtm) REVERT: B 794 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7845 (mp0) REVERT: B 826 ASN cc_start: 0.8881 (m110) cc_final: 0.8555 (m110) REVERT: B 828 GLU cc_start: 0.8397 (pm20) cc_final: 0.8138 (pm20) REVERT: B 886 LYS cc_start: 0.8388 (mppt) cc_final: 0.8151 (mptt) REVERT: D 62 GLU cc_start: 0.8480 (tp30) cc_final: 0.8027 (tp30) REVERT: E 87 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8125 (tm-30) REVERT: F 57 ASP cc_start: 0.7795 (t0) cc_final: 0.7321 (t0) REVERT: F 119 LEU cc_start: 0.8544 (mt) cc_final: 0.8184 (mm) REVERT: F 122 ASP cc_start: 0.6732 (m-30) cc_final: 0.6422 (m-30) REVERT: G 63 ASP cc_start: 0.7828 (p0) cc_final: 0.7499 (p0) REVERT: G 171 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8062 (mm-30) REVERT: G 174 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8324 (ttm110) outliers start: 63 outliers final: 31 residues processed: 544 average time/residue: 1.7033 time to fit residues: 1042.6387 Evaluate side-chains 529 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 494 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 691 TYR Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 1031 CYS Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 279 optimal weight: 0.0870 chunk 212 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 208 GLN A1030 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN G 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091774 restraints weight = 49491.687| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.67 r_work: 0.3373 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24382 Z= 0.141 Angle : 0.619 10.070 32973 Z= 0.314 Chirality : 0.040 0.144 3738 Planarity : 0.004 0.052 4188 Dihedral : 6.267 149.418 3273 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.97 % Allowed : 19.11 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.16), residues: 2920 helix: 2.49 (0.12), residues: 1957 sheet: 1.20 (0.48), residues: 109 loop : -0.18 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 97 HIS 0.004 0.001 HIS A 261 PHE 0.015 0.001 PHE B 521 TYR 0.025 0.001 TYR B 930 ARG 0.008 0.001 ARG A 597 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 1539) hydrogen bonds : angle 3.80617 ( 4467) covalent geometry : bond 0.00319 (24382) covalent geometry : angle 0.61895 (32973) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 503 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8436 (mmm) cc_final: 0.7964 (mmm) REVERT: A 72 MET cc_start: 0.8511 (ttm) cc_final: 0.8229 (ttm) REVERT: A 74 GLU cc_start: 0.8294 (pp20) cc_final: 0.7322 (pp20) REVERT: A 75 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 78 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: A 114 VAL cc_start: 0.8913 (t) cc_final: 0.8543 (p) REVERT: A 134 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 135 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7775 (ttm-80) REVERT: A 206 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8189 (mm-30) REVERT: A 310 ASP cc_start: 0.8579 (t0) cc_final: 0.7876 (t0) REVERT: A 351 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8154 (mm-40) REVERT: A 446 GLU cc_start: 0.8375 (mp0) cc_final: 0.7930 (pm20) REVERT: A 447 GLU cc_start: 0.7915 (mp0) cc_final: 0.7581 (mp0) REVERT: A 546 LYS cc_start: 0.8039 (pptt) cc_final: 0.7813 (pptt) REVERT: A 597 ARG cc_start: 0.7212 (ttp80) cc_final: 0.7011 (ttp80) REVERT: A 598 GLU cc_start: 0.8034 (tp30) cc_final: 0.7642 (tp30) REVERT: A 614 GLN cc_start: 0.8619 (tt0) cc_final: 0.8271 (tm-30) REVERT: A 641 GLU cc_start: 0.7888 (pp20) cc_final: 0.7504 (pp20) REVERT: A 730 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8300 (tp30) REVERT: A 747 GLU cc_start: 0.8132 (mp0) cc_final: 0.7828 (mp0) REVERT: A 807 MET cc_start: 0.8756 (tpp) cc_final: 0.8280 (ttp) REVERT: A 878 ASP cc_start: 0.8224 (t0) cc_final: 0.7911 (t0) REVERT: A 961 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8220 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8070 (pp20) REVERT: A 1030 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8034 (t0) REVERT: A 1043 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7937 (tm) REVERT: A 1084 GLU cc_start: 0.7816 (pp20) cc_final: 0.7326 (pp20) REVERT: A 1163 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8193 (ttp) REVERT: A 1178 ASP cc_start: 0.7753 (t0) cc_final: 0.7278 (t0) REVERT: A 1193 ASP cc_start: 0.7971 (t70) cc_final: 0.7644 (t0) REVERT: A 1216 ASP cc_start: 0.8447 (p0) cc_final: 0.8174 (p0) REVERT: B 51 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7710 (mmmt) REVERT: B 78 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7452 (tm-30) REVERT: B 122 ASP cc_start: 0.7965 (t0) cc_final: 0.7382 (t0) REVERT: B 151 GLU cc_start: 0.7488 (tp30) cc_final: 0.7189 (tm-30) REVERT: B 211 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7637 (tp-100) REVERT: B 352 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7940 (tp30) REVERT: B 413 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 414 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 479 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 510 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6112 (mtp85) REVERT: B 531 GLU cc_start: 0.8288 (mp0) cc_final: 0.7896 (mp0) REVERT: B 558 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 725 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8267 (mtm) REVERT: B 794 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7864 (mp0) REVERT: B 826 ASN cc_start: 0.8874 (m110) cc_final: 0.8545 (m110) REVERT: B 828 GLU cc_start: 0.8388 (pm20) cc_final: 0.8148 (pm20) REVERT: B 886 LYS cc_start: 0.8391 (mppt) cc_final: 0.7908 (mppt) REVERT: C 71 GLU cc_start: 0.8223 (tp30) cc_final: 0.7898 (tp30) REVERT: C 75 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8190 (ttm-80) REVERT: C 83 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7341 (tp) REVERT: D 62 GLU cc_start: 0.8451 (tp30) cc_final: 0.7983 (tp30) REVERT: E 42 ASP cc_start: 0.7113 (t0) cc_final: 0.6611 (t0) REVERT: E 87 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 107 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8124 (ttm110) REVERT: E 120 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7588 (mmm-85) REVERT: F 57 ASP cc_start: 0.7724 (t0) cc_final: 0.7350 (t0) REVERT: F 119 LEU cc_start: 0.8535 (mt) cc_final: 0.8174 (mm) REVERT: F 122 ASP cc_start: 0.6711 (m-30) cc_final: 0.6387 (m-30) REVERT: F 168 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8382 (m) REVERT: G 63 ASP cc_start: 0.7804 (p0) cc_final: 0.7549 (p0) REVERT: G 158 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8333 (p) REVERT: G 170 ASP cc_start: 0.8201 (t0) cc_final: 0.7939 (OUTLIER) REVERT: G 171 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8077 (mm-30) REVERT: G 174 ARG cc_start: 0.8591 (ttm110) cc_final: 0.8311 (ttm110) outliers start: 79 outliers final: 24 residues processed: 547 average time/residue: 1.6338 time to fit residues: 1003.3099 Evaluate side-chains 529 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 497 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 1031 CYS Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 151 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 GLN A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN G 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091223 restraints weight = 49107.438| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.65 r_work: 0.3362 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24382 Z= 0.148 Angle : 0.644 12.745 32973 Z= 0.323 Chirality : 0.040 0.171 3738 Planarity : 0.004 0.052 4188 Dihedral : 6.267 149.508 3273 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.52 % Allowed : 20.23 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.16), residues: 2920 helix: 2.45 (0.12), residues: 1953 sheet: 1.12 (0.47), residues: 109 loop : -0.17 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 97 HIS 0.006 0.001 HIS A1058 PHE 0.016 0.001 PHE B 521 TYR 0.027 0.001 TYR F 154 ARG 0.010 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1539) hydrogen bonds : angle 3.78217 ( 4467) covalent geometry : bond 0.00335 (24382) covalent geometry : angle 0.64404 (32973) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 514 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8430 (mmm) cc_final: 0.7962 (mmm) REVERT: A 72 MET cc_start: 0.8536 (ttm) cc_final: 0.8261 (ttm) REVERT: A 74 GLU cc_start: 0.8302 (pp20) cc_final: 0.7339 (pp20) REVERT: A 75 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 78 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7745 (pp20) REVERT: A 114 VAL cc_start: 0.8888 (t) cc_final: 0.8528 (p) REVERT: A 134 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 206 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8177 (mm-30) REVERT: A 262 MET cc_start: 0.7947 (tmm) cc_final: 0.7681 (tmm) REVERT: A 301 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 310 ASP cc_start: 0.8554 (t0) cc_final: 0.7887 (t0) REVERT: A 351 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8188 (mm-40) REVERT: A 446 GLU cc_start: 0.8371 (mp0) cc_final: 0.7818 (pm20) REVERT: A 447 GLU cc_start: 0.7948 (mp0) cc_final: 0.7340 (mp0) REVERT: A 546 LYS cc_start: 0.8155 (pptt) cc_final: 0.7597 (pptt) REVERT: A 593 GLU cc_start: 0.7684 (pp20) cc_final: 0.7473 (pp20) REVERT: A 597 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6871 (ttp80) REVERT: A 598 GLU cc_start: 0.8047 (tp30) cc_final: 0.7452 (tm-30) REVERT: A 614 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: A 730 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8343 (tp30) REVERT: A 803 GLU cc_start: 0.8054 (pp20) cc_final: 0.7848 (pp20) REVERT: A 807 MET cc_start: 0.8774 (tpp) cc_final: 0.8105 (ttp) REVERT: A 878 ASP cc_start: 0.8262 (t0) cc_final: 0.7949 (t0) REVERT: A 961 ARG cc_start: 0.8442 (mtt90) cc_final: 0.8225 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7964 (pp20) REVERT: A 1030 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.7688 (t0) REVERT: A 1043 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7971 (tm) REVERT: A 1084 GLU cc_start: 0.7833 (pp20) cc_final: 0.7294 (pp20) REVERT: A 1092 MET cc_start: 0.7809 (ptp) cc_final: 0.7242 (ptm) REVERT: A 1163 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: A 1178 ASP cc_start: 0.7765 (t0) cc_final: 0.7289 (t0) REVERT: A 1193 ASP cc_start: 0.8003 (t70) cc_final: 0.7669 (t0) REVERT: A 1216 ASP cc_start: 0.8464 (p0) cc_final: 0.8169 (p0) REVERT: B 51 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7764 (mmmt) REVERT: B 78 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7450 (tm-30) REVERT: B 122 ASP cc_start: 0.7983 (t0) cc_final: 0.7404 (t0) REVERT: B 151 GLU cc_start: 0.7241 (tp30) cc_final: 0.6993 (tm-30) REVERT: B 211 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7689 (tp-100) REVERT: B 230 LEU cc_start: 0.9105 (mt) cc_final: 0.8899 (mm) REVERT: B 276 ASP cc_start: 0.8217 (t0) cc_final: 0.8011 (t0) REVERT: B 338 MET cc_start: 0.8568 (tmt) cc_final: 0.8327 (tmt) REVERT: B 352 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7957 (tp30) REVERT: B 407 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7620 (mm-30) REVERT: B 413 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 414 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 479 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7256 (tm-30) REVERT: B 510 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6106 (mtp85) REVERT: B 531 GLU cc_start: 0.8311 (mp0) cc_final: 0.7914 (mp0) REVERT: B 725 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: B 826 ASN cc_start: 0.8879 (m110) cc_final: 0.8543 (m110) REVERT: B 828 GLU cc_start: 0.8388 (pm20) cc_final: 0.8181 (pm20) REVERT: B 841 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7920 (tp30) REVERT: B 886 LYS cc_start: 0.8418 (mppt) cc_final: 0.8002 (mppt) REVERT: C 71 GLU cc_start: 0.8307 (tp30) cc_final: 0.7894 (tp30) REVERT: C 75 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8172 (ttm-80) REVERT: C 83 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7369 (tp) REVERT: D 47 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7270 (mp) REVERT: D 62 GLU cc_start: 0.8440 (tp30) cc_final: 0.8002 (tp30) REVERT: D 65 GLU cc_start: 0.8127 (tp30) cc_final: 0.7912 (tp30) REVERT: E 87 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 120 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7604 (mmm-85) REVERT: F 57 ASP cc_start: 0.7675 (t0) cc_final: 0.7394 (t0) REVERT: F 119 LEU cc_start: 0.8504 (mt) cc_final: 0.8159 (mm) REVERT: F 122 ASP cc_start: 0.6747 (m-30) cc_final: 0.6397 (m-30) REVERT: F 168 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8375 (m) REVERT: G 11 ASP cc_start: 0.8213 (t0) cc_final: 0.8009 (t0) REVERT: G 63 ASP cc_start: 0.7792 (p0) cc_final: 0.7570 (p0) REVERT: G 122 ASP cc_start: 0.6220 (t0) cc_final: 0.5992 (t0) REVERT: G 158 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (p) REVERT: G 170 ASP cc_start: 0.8179 (t0) cc_final: 0.7970 (t0) outliers start: 67 outliers final: 32 residues processed: 546 average time/residue: 1.6424 time to fit residues: 1006.4762 Evaluate side-chains 539 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 496 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 1031 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 156 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 356 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090491 restraints weight = 50511.527| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.73 r_work: 0.3353 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24382 Z= 0.146 Angle : 0.664 11.732 32973 Z= 0.332 Chirality : 0.040 0.174 3738 Planarity : 0.004 0.054 4188 Dihedral : 6.275 149.382 3273 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.52 % Allowed : 21.25 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2920 helix: 2.45 (0.12), residues: 1955 sheet: 0.94 (0.46), residues: 119 loop : -0.21 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 97 HIS 0.005 0.001 HIS A1058 PHE 0.027 0.001 PHE G 28 TYR 0.026 0.001 TYR B 930 ARG 0.012 0.001 ARG G 174 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 1539) hydrogen bonds : angle 3.77568 ( 4467) covalent geometry : bond 0.00335 (24382) covalent geometry : angle 0.66436 (32973) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 509 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8363 (mmm) cc_final: 0.7890 (mmm) REVERT: A 72 MET cc_start: 0.8550 (ttm) cc_final: 0.8263 (ttm) REVERT: A 74 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: A 75 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 78 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: A 114 VAL cc_start: 0.8840 (t) cc_final: 0.8463 (p) REVERT: A 118 GLU cc_start: 0.7238 (pp20) cc_final: 0.6918 (pp20) REVERT: A 134 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 206 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8133 (mm-30) REVERT: A 262 MET cc_start: 0.7961 (tmm) cc_final: 0.7692 (tmm) REVERT: A 274 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7892 (mtm) REVERT: A 288 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8271 (mptt) REVERT: A 310 ASP cc_start: 0.8644 (t0) cc_final: 0.7571 (t0) REVERT: A 351 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8175 (mm-40) REVERT: A 447 GLU cc_start: 0.7991 (mp0) cc_final: 0.7672 (mp0) REVERT: A 593 GLU cc_start: 0.7691 (pp20) cc_final: 0.7457 (pp20) REVERT: A 597 ARG cc_start: 0.7218 (ttp80) cc_final: 0.6790 (ttp80) REVERT: A 598 GLU cc_start: 0.8087 (tp30) cc_final: 0.7468 (tm-30) REVERT: A 614 GLN cc_start: 0.8595 (tt0) cc_final: 0.8287 (tm-30) REVERT: A 730 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8022 (tp30) REVERT: A 734 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8668 (tp40) REVERT: A 747 GLU cc_start: 0.8052 (mp0) cc_final: 0.7706 (mp0) REVERT: A 878 ASP cc_start: 0.8331 (t0) cc_final: 0.7983 (t0) REVERT: A 961 ARG cc_start: 0.8543 (mtt90) cc_final: 0.8321 (mtt-85) REVERT: A 1011 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7507 (tt0) REVERT: A 1017 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7843 (pp20) REVERT: A 1030 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7736 (t0) REVERT: A 1043 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7948 (tm) REVERT: A 1083 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8339 (ptpp) REVERT: A 1084 GLU cc_start: 0.7824 (pp20) cc_final: 0.7219 (pp20) REVERT: A 1163 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: A 1193 ASP cc_start: 0.8077 (t70) cc_final: 0.7737 (t0) REVERT: A 1216 ASP cc_start: 0.8460 (p0) cc_final: 0.8144 (p0) REVERT: B 51 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7780 (mmmt) REVERT: B 78 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7408 (tm-30) REVERT: B 122 ASP cc_start: 0.7984 (t0) cc_final: 0.7434 (t0) REVERT: B 211 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7731 (tp-100) REVERT: B 352 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7807 (tp30) REVERT: B 413 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 414 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 479 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 510 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6003 (mtp85) REVERT: B 531 GLU cc_start: 0.8317 (mp0) cc_final: 0.7894 (mp0) REVERT: B 682 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 725 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8330 (mtm) REVERT: B 794 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7803 (mp0) REVERT: B 826 ASN cc_start: 0.8842 (m110) cc_final: 0.8473 (m110) REVERT: B 828 GLU cc_start: 0.8445 (pm20) cc_final: 0.8174 (pm20) REVERT: B 886 LYS cc_start: 0.8367 (mppt) cc_final: 0.8090 (mptt) REVERT: C 83 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7358 (tp) REVERT: D 47 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7047 (mp) REVERT: D 62 GLU cc_start: 0.8448 (tp30) cc_final: 0.8064 (tp30) REVERT: D 65 GLU cc_start: 0.8086 (tp30) cc_final: 0.7837 (tp30) REVERT: E 42 ASP cc_start: 0.6901 (t0) cc_final: 0.6491 (t0) REVERT: E 87 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8110 (tm-30) REVERT: E 107 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7821 (ttm170) REVERT: F 57 ASP cc_start: 0.7779 (t0) cc_final: 0.7475 (t0) REVERT: F 119 LEU cc_start: 0.8477 (mt) cc_final: 0.8131 (mm) REVERT: F 122 ASP cc_start: 0.6794 (m-30) cc_final: 0.6432 (m-30) REVERT: F 168 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8294 (m) REVERT: G 11 ASP cc_start: 0.8238 (t0) cc_final: 0.8011 (t0) REVERT: G 63 ASP cc_start: 0.7823 (p0) cc_final: 0.7587 (p0) REVERT: G 122 ASP cc_start: 0.6196 (t0) cc_final: 0.5908 (t0) REVERT: G 158 SER cc_start: 0.8783 (m) cc_final: 0.8480 (p) outliers start: 67 outliers final: 35 residues processed: 541 average time/residue: 1.6414 time to fit residues: 997.8827 Evaluate side-chains 546 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 498 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1083 LYS Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1031 CYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 614 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.088975 restraints weight = 50344.031| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.71 r_work: 0.3325 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24382 Z= 0.170 Angle : 0.706 11.448 32973 Z= 0.354 Chirality : 0.042 0.245 3738 Planarity : 0.004 0.062 4188 Dihedral : 6.311 149.775 3273 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.67 % Allowed : 21.96 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2920 helix: 2.41 (0.12), residues: 1949 sheet: 1.03 (0.46), residues: 109 loop : -0.24 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 97 HIS 0.007 0.001 HIS A1058 PHE 0.023 0.001 PHE G 28 TYR 0.029 0.001 TYR F 154 ARG 0.014 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 1539) hydrogen bonds : angle 3.80986 ( 4467) covalent geometry : bond 0.00399 (24382) covalent geometry : angle 0.70608 (32973) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 514 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8378 (mmm) cc_final: 0.7921 (mmm) REVERT: A 72 MET cc_start: 0.8557 (ttm) cc_final: 0.8317 (ttm) REVERT: A 74 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: A 75 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 78 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: A 114 VAL cc_start: 0.8814 (t) cc_final: 0.8415 (p) REVERT: A 134 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 148 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7329 (ttm-80) REVERT: A 262 MET cc_start: 0.8007 (tmm) cc_final: 0.7757 (tmm) REVERT: A 274 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: A 310 ASP cc_start: 0.8524 (t0) cc_final: 0.7893 (t0) REVERT: A 351 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8158 (mm-40) REVERT: A 447 GLU cc_start: 0.8054 (mp0) cc_final: 0.7691 (mp0) REVERT: A 546 LYS cc_start: 0.8340 (pptt) cc_final: 0.7943 (pptt) REVERT: A 597 ARG cc_start: 0.7223 (ttp80) cc_final: 0.6832 (ttp80) REVERT: A 598 GLU cc_start: 0.8087 (tp30) cc_final: 0.7479 (tm-30) REVERT: A 614 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: A 641 GLU cc_start: 0.8055 (pp20) cc_final: 0.7768 (pp20) REVERT: A 730 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8040 (tp30) REVERT: A 734 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8642 (tp40) REVERT: A 747 GLU cc_start: 0.8065 (mp0) cc_final: 0.7832 (mp0) REVERT: A 763 ASP cc_start: 0.8127 (t0) cc_final: 0.7851 (t70) REVERT: A 807 MET cc_start: 0.8753 (tpp) cc_final: 0.8321 (ttp) REVERT: A 878 ASP cc_start: 0.8367 (t0) cc_final: 0.8025 (t0) REVERT: A 961 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8339 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8014 (pp20) REVERT: A 1030 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 1083 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8305 (ptpp) REVERT: A 1084 GLU cc_start: 0.7883 (pp20) cc_final: 0.7275 (pp20) REVERT: A 1163 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: A 1178 ASP cc_start: 0.7857 (t0) cc_final: 0.7315 (t0) REVERT: A 1193 ASP cc_start: 0.8069 (t70) cc_final: 0.7743 (t0) REVERT: A 1216 ASP cc_start: 0.8445 (p0) cc_final: 0.8127 (p0) REVERT: B 51 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7776 (mmmt) REVERT: B 78 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7455 (tm-30) REVERT: B 122 ASP cc_start: 0.8035 (t0) cc_final: 0.7462 (t0) REVERT: B 151 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6968 (tm-30) REVERT: B 211 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7783 (tp-100) REVERT: B 352 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7829 (tp30) REVERT: B 413 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 414 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 479 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B 510 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6070 (mtp85) REVERT: B 531 GLU cc_start: 0.8343 (mp0) cc_final: 0.7949 (mp0) REVERT: B 794 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7827 (mp0) REVERT: B 826 ASN cc_start: 0.8867 (m110) cc_final: 0.8499 (m110) REVERT: B 828 GLU cc_start: 0.8457 (pm20) cc_final: 0.8179 (pm20) REVERT: B 841 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8059 (tp30) REVERT: B 886 LYS cc_start: 0.8405 (mppt) cc_final: 0.8158 (mptt) REVERT: B 1078 THR cc_start: 0.9102 (p) cc_final: 0.8765 (t) REVERT: C 71 GLU cc_start: 0.8319 (tp30) cc_final: 0.7992 (tp30) REVERT: C 75 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8195 (ttm-80) REVERT: C 83 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7408 (tp) REVERT: D 47 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7085 (mp) REVERT: D 62 GLU cc_start: 0.8435 (tp30) cc_final: 0.8011 (tp30) REVERT: D 65 GLU cc_start: 0.8147 (tp30) cc_final: 0.7842 (tp30) REVERT: E 87 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 57 ASP cc_start: 0.7791 (t0) cc_final: 0.7485 (t0) REVERT: F 119 LEU cc_start: 0.8456 (mt) cc_final: 0.8109 (mm) REVERT: F 122 ASP cc_start: 0.6853 (m-30) cc_final: 0.6474 (m-30) REVERT: F 153 LYS cc_start: 0.7073 (tppp) cc_final: 0.6783 (tppp) REVERT: F 168 VAL cc_start: 0.8595 (p) cc_final: 0.8352 (m) REVERT: G 122 ASP cc_start: 0.6256 (t0) cc_final: 0.6013 (t0) REVERT: G 158 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8567 (p) REVERT: G 174 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8155 (ttm110) outliers start: 71 outliers final: 36 residues processed: 546 average time/residue: 1.7272 time to fit residues: 1060.0748 Evaluate side-chains 547 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 499 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1083 LYS Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 271 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 266 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN C 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.100751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090053 restraints weight = 50207.086| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.72 r_work: 0.3342 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24382 Z= 0.149 Angle : 0.731 13.269 32973 Z= 0.362 Chirality : 0.040 0.174 3738 Planarity : 0.004 0.054 4188 Dihedral : 6.299 151.198 3269 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 23.35 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2920 helix: 2.48 (0.12), residues: 1940 sheet: 1.01 (0.46), residues: 109 loop : -0.25 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 97 HIS 0.008 0.001 HIS A1058 PHE 0.024 0.001 PHE B 521 TYR 0.033 0.001 TYR F 154 ARG 0.010 0.001 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 1539) hydrogen bonds : angle 3.77342 ( 4467) covalent geometry : bond 0.00346 (24382) covalent geometry : angle 0.73079 (32973) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 510 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8398 (mmm) cc_final: 0.7939 (mmm) REVERT: A 72 MET cc_start: 0.8589 (ttm) cc_final: 0.8323 (ttm) REVERT: A 74 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: A 75 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7908 (mm-30) REVERT: A 78 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7732 (pp20) REVERT: A 148 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7334 (ttm-80) REVERT: A 274 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: A 275 ASP cc_start: 0.8038 (m-30) cc_final: 0.7726 (t0) REVERT: A 310 ASP cc_start: 0.8486 (t0) cc_final: 0.8164 (t0) REVERT: A 351 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8127 (mm-40) REVERT: A 447 GLU cc_start: 0.8046 (mp0) cc_final: 0.7657 (mp0) REVERT: A 597 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6933 (ttp80) REVERT: A 598 GLU cc_start: 0.8097 (tp30) cc_final: 0.7525 (tm-30) REVERT: A 631 THR cc_start: 0.8695 (m) cc_final: 0.8331 (t) REVERT: A 684 LYS cc_start: 0.8936 (mmtp) cc_final: 0.8723 (mmtm) REVERT: A 730 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8276 (tp30) REVERT: A 734 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8792 (tp40) REVERT: A 807 MET cc_start: 0.8783 (tpp) cc_final: 0.8300 (ttp) REVERT: A 878 ASP cc_start: 0.8365 (t0) cc_final: 0.8047 (t0) REVERT: A 961 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8311 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8051 (pp20) REVERT: A 1030 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7823 (t0) REVERT: A 1083 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8348 (ptpp) REVERT: A 1084 GLU cc_start: 0.7854 (pp20) cc_final: 0.7256 (pp20) REVERT: A 1092 MET cc_start: 0.7338 (ptm) cc_final: 0.6997 (ptp) REVERT: A 1163 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: A 1178 ASP cc_start: 0.7825 (t0) cc_final: 0.7334 (t0) REVERT: A 1193 ASP cc_start: 0.8019 (t70) cc_final: 0.7691 (t0) REVERT: A 1216 ASP cc_start: 0.8458 (p0) cc_final: 0.8157 (p0) REVERT: B 51 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7816 (mmmt) REVERT: B 78 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7497 (tm-30) REVERT: B 122 ASP cc_start: 0.7958 (t0) cc_final: 0.7369 (t0) REVERT: B 211 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7856 (tp-100) REVERT: B 338 MET cc_start: 0.8489 (tmt) cc_final: 0.8206 (tmt) REVERT: B 352 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7852 (tp30) REVERT: B 392 MET cc_start: 0.8187 (tmm) cc_final: 0.7975 (ppp) REVERT: B 407 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7800 (mm-30) REVERT: B 413 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 414 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 479 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 510 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6021 (mtp85) REVERT: B 531 GLU cc_start: 0.8349 (mp0) cc_final: 0.8102 (mp0) REVERT: B 794 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7873 (mp0) REVERT: B 826 ASN cc_start: 0.8873 (m110) cc_final: 0.8523 (m110) REVERT: B 828 GLU cc_start: 0.8419 (pm20) cc_final: 0.8176 (pm20) REVERT: B 886 LYS cc_start: 0.8441 (mppt) cc_final: 0.8192 (mptt) REVERT: B 1075 LYS cc_start: 0.8402 (tmmm) cc_final: 0.8160 (tmmt) REVERT: B 1078 THR cc_start: 0.9076 (p) cc_final: 0.8712 (t) REVERT: C 71 GLU cc_start: 0.8344 (tp30) cc_final: 0.8038 (tp30) REVERT: C 75 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8227 (ttm-80) REVERT: C 83 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7476 (tp) REVERT: D 62 GLU cc_start: 0.8412 (tp30) cc_final: 0.8000 (tp30) REVERT: D 65 GLU cc_start: 0.8156 (tp30) cc_final: 0.7860 (tp30) REVERT: E 87 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8185 (tm-30) REVERT: F 57 ASP cc_start: 0.7780 (t0) cc_final: 0.7494 (t0) REVERT: F 119 LEU cc_start: 0.8423 (mt) cc_final: 0.8036 (mm) REVERT: F 122 ASP cc_start: 0.6803 (m-30) cc_final: 0.6432 (m-30) REVERT: G 122 ASP cc_start: 0.6284 (t0) cc_final: 0.6042 (t0) REVERT: G 158 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8635 (p) REVERT: G 170 ASP cc_start: 0.8102 (t0) cc_final: 0.7898 (t0) REVERT: G 174 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8156 (ttm110) outliers start: 52 outliers final: 28 residues processed: 533 average time/residue: 1.6181 time to fit residues: 974.9344 Evaluate side-chains 539 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 501 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1083 LYS Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 210 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 179 optimal weight: 0.0980 chunk 213 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 203 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS B 766 ASN ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.102600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091854 restraints weight = 50480.104| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.74 r_work: 0.3367 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24382 Z= 0.144 Angle : 0.748 12.603 32973 Z= 0.371 Chirality : 0.040 0.240 3738 Planarity : 0.004 0.073 4188 Dihedral : 6.314 154.879 3269 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.58 % Allowed : 23.95 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.16), residues: 2920 helix: 2.48 (0.12), residues: 1954 sheet: 1.08 (0.46), residues: 109 loop : -0.26 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 97 HIS 0.008 0.001 HIS A1058 PHE 0.022 0.001 PHE G 28 TYR 0.026 0.001 TYR B 930 ARG 0.014 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 1539) hydrogen bonds : angle 3.74930 ( 4467) covalent geometry : bond 0.00327 (24382) covalent geometry : angle 0.74797 (32973) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 516 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8353 (mmm) cc_final: 0.7938 (mmm) REVERT: A 74 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7358 (pp20) REVERT: A 75 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 114 VAL cc_start: 0.8906 (t) cc_final: 0.8630 (p) REVERT: A 118 GLU cc_start: 0.7150 (pp20) cc_final: 0.6788 (pp20) REVERT: A 148 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7322 (ttm-80) REVERT: A 274 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: A 275 ASP cc_start: 0.8042 (m-30) cc_final: 0.7713 (t0) REVERT: A 310 ASP cc_start: 0.8487 (t0) cc_final: 0.8192 (t0) REVERT: A 351 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8080 (mm-40) REVERT: A 447 GLU cc_start: 0.7950 (mp0) cc_final: 0.7691 (mp0) REVERT: A 597 ARG cc_start: 0.7160 (ttp80) cc_final: 0.6876 (ttp80) REVERT: A 598 GLU cc_start: 0.8149 (tp30) cc_final: 0.7583 (tm-30) REVERT: A 631 THR cc_start: 0.8737 (m) cc_final: 0.8371 (t) REVERT: A 684 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8345 (mptp) REVERT: A 730 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8334 (tp30) REVERT: A 807 MET cc_start: 0.8799 (tpp) cc_final: 0.8340 (ttp) REVERT: A 878 ASP cc_start: 0.8382 (t0) cc_final: 0.8048 (t0) REVERT: A 961 ARG cc_start: 0.8530 (mtt90) cc_final: 0.8317 (mtt-85) REVERT: A 1017 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8020 (pp20) REVERT: A 1030 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8124 (p0) REVERT: A 1083 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8243 (ptpp) REVERT: A 1084 GLU cc_start: 0.7784 (pp20) cc_final: 0.7163 (pp20) REVERT: A 1163 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8282 (ttp) REVERT: A 1178 ASP cc_start: 0.7728 (t0) cc_final: 0.7235 (t0) REVERT: A 1193 ASP cc_start: 0.8050 (t70) cc_final: 0.7665 (t0) REVERT: A 1216 ASP cc_start: 0.8479 (p0) cc_final: 0.8168 (p0) REVERT: B 51 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7790 (mmmt) REVERT: B 78 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7480 (tm-30) REVERT: B 152 GLU cc_start: 0.7181 (mp0) cc_final: 0.6866 (pm20) REVERT: B 351 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8572 (tppp) REVERT: B 352 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7821 (tp30) REVERT: B 392 MET cc_start: 0.8202 (tmm) cc_final: 0.7962 (ppp) REVERT: B 407 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7607 (mm-30) REVERT: B 413 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 414 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 444 GLU cc_start: 0.7942 (pp20) cc_final: 0.7551 (pp20) REVERT: B 479 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7189 (tm-30) REVERT: B 531 GLU cc_start: 0.8355 (mp0) cc_final: 0.8096 (mp0) REVERT: B 593 ASP cc_start: 0.8225 (m-30) cc_final: 0.7924 (m-30) REVERT: B 731 GLN cc_start: 0.8231 (tt0) cc_final: 0.7804 (tm-30) REVERT: B 794 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7850 (mp0) REVERT: B 826 ASN cc_start: 0.8819 (m110) cc_final: 0.8471 (m110) REVERT: B 828 GLU cc_start: 0.8418 (pm20) cc_final: 0.8125 (pm20) REVERT: B 841 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8030 (tp30) REVERT: B 886 LYS cc_start: 0.8389 (mppt) cc_final: 0.7972 (mppt) REVERT: B 959 TYR cc_start: 0.8604 (m-10) cc_final: 0.8276 (m-80) REVERT: B 1075 LYS cc_start: 0.8361 (tmmm) cc_final: 0.8107 (tmmt) REVERT: B 1078 THR cc_start: 0.9053 (p) cc_final: 0.8704 (t) REVERT: C 71 GLU cc_start: 0.8334 (tp30) cc_final: 0.8011 (tp30) REVERT: C 75 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8213 (ttm-80) REVERT: C 83 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7477 (tp) REVERT: D 62 GLU cc_start: 0.8395 (tp30) cc_final: 0.7986 (tp30) REVERT: D 68 VAL cc_start: 0.7362 (t) cc_final: 0.7034 (p) REVERT: E 87 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8135 (tm-30) REVERT: F 57 ASP cc_start: 0.7698 (t0) cc_final: 0.7403 (t0) REVERT: F 119 LEU cc_start: 0.8417 (mt) cc_final: 0.8062 (mm) REVERT: F 122 ASP cc_start: 0.6762 (m-30) cc_final: 0.6374 (m-30) REVERT: F 143 LEU cc_start: 0.4656 (OUTLIER) cc_final: 0.4291 (mt) REVERT: F 153 LYS cc_start: 0.7037 (ttmm) cc_final: 0.6613 (ttpp) REVERT: F 156 GLU cc_start: 0.8369 (mp0) cc_final: 0.8148 (mm-30) REVERT: G 122 ASP cc_start: 0.6297 (t0) cc_final: 0.6045 (t0) REVERT: G 158 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8652 (p) REVERT: G 170 ASP cc_start: 0.8094 (t0) cc_final: 0.7891 (t0) REVERT: G 174 ARG cc_start: 0.8380 (ttm110) cc_final: 0.8139 (ttm110) outliers start: 42 outliers final: 29 residues processed: 536 average time/residue: 1.6114 time to fit residues: 972.9289 Evaluate side-chains 537 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 499 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1083 LYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 125 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 24 optimal weight: 0.0270 chunk 280 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN A 473 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.101846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091212 restraints weight = 50464.375| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.72 r_work: 0.3363 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24382 Z= 0.148 Angle : 0.764 12.129 32973 Z= 0.379 Chirality : 0.040 0.249 3738 Planarity : 0.004 0.053 4188 Dihedral : 6.296 154.260 3269 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.54 % Allowed : 24.70 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.16), residues: 2920 helix: 2.46 (0.12), residues: 1953 sheet: 1.06 (0.45), residues: 109 loop : -0.28 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 97 HIS 0.006 0.001 HIS A 407 PHE 0.033 0.001 PHE B 521 TYR 0.028 0.001 TYR F 154 ARG 0.013 0.001 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 1539) hydrogen bonds : angle 3.75884 ( 4467) covalent geometry : bond 0.00345 (24382) covalent geometry : angle 0.76386 (32973) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21802.05 seconds wall clock time: 374 minutes 15.18 seconds (22455.18 seconds total)