Starting phenix.real_space_refine on Tue Mar 19 10:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/03_2024/7use_26734_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/03_2024/7use_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/03_2024/7use_26734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/03_2024/7use_26734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/03_2024/7use_26734_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/03_2024/7use_26734_updated.pdb" } 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 Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.90, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 10.37 Conformation dependent library (CDL) restraints added in 4.4 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... running ksdssp... Secondary structure from input PDB file: 142 helices and 7 sheets defined 66.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 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) Processing helix chain 'A' and resid 57 through 84 removed outlier: 3.688A pdb=" N GLN A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 117 through 143 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 150 Processing helix chain 'A' and resid 155 through 177 Processing helix chain 'A' and resid 180 through 195 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 234 through 250 Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.670A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.179A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 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) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.672A pdb=" N MET A 349 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 351 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 358 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 359 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 365 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 417 Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 445 through 489 removed outlier: 4.969A pdb=" N SER A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 501 Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.585A pdb=" N VAL A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 No H-bonds generated for 'chain 'A' and resid 531 through 534' Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.908A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 600 through 606 removed outlier: 4.104A pdb=" N THR A 603 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 625 through 631 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.557A pdb=" N VAL A 664 " --> pdb=" O MET A 661 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 665 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP A 669 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 670 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 671 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 680 " --> pdb=" O TYR A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 722 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 725 through 734 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 764 through 789 Processing helix chain 'A' and resid 792 through 814 removed outlier: 3.500A pdb=" N ILE A 795 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 796 " --> pdb=" O THR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 829 Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 885 through 887 No H-bonds generated for 'chain 'A' and resid 885 through 887' Processing helix chain 'A' and resid 892 through 905 removed outlier: 3.509A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 924 through 942 Processing helix chain 'A' and resid 944 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 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.661A pdb=" N GLU A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 985 Processing helix chain 'A' and resid 988 through 990 No H-bonds generated for 'chain 'A' and resid 988 through 990' Processing helix chain 'A' and resid 993 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 1027 through 1029 No H-bonds generated for 'chain 'A' and resid 1027 through 1029' Processing helix chain 'A' and resid 1043 through 1053 Processing helix chain 'A' and resid 1055 through 1057 No H-bonds generated for 'chain 'A' and resid 1055 through 1057' Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1069 through 1083 Processing helix chain 'A' and resid 1093 through 1103 Processing helix chain 'A' and resid 1107 through 1110 No H-bonds generated for 'chain 'A' and resid 1107 through 1110' Processing helix chain 'A' and resid 1127 through 1138 Processing helix chain 'A' and resid 1149 through 1152 No H-bonds generated for 'chain 'A' and resid 1149 through 1152' Processing helix chain 'A' and resid 1156 through 1167 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1179 through 1190 Processing helix chain 'A' and resid 1201 through 1225 Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.565A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 77 through 89 removed outlier: 4.280A pdb=" N LYS B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 Processing helix chain 'B' and resid 127 through 149 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.753A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.664A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N MET B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 No H-bonds generated for 'chain 'B' and resid 214 through 217' Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 248 through 252 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 248 through 252' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.856A pdb=" N ASN B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 318 through 359 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 366 removed outlier: 3.822A pdb=" N GLY B 365 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Proline residue: B 366 - end of helix Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.942A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 454 through 469 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 476 removed outlier: 4.134A pdb=" N GLU B 476 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 507 through 527 removed outlier: 3.920A pdb=" N ARG B 510 " --> pdb=" O ALA B 507 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU B 511 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 527 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 561 through 579 removed outlier: 4.015A pdb=" N ARG B 564 " --> pdb=" O SER B 561 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) Proline residue: B 570 - end of helix 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) Processing helix chain 'B' and resid 585 through 628 removed outlier: 3.830A pdb=" N HIS B 589 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 598 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 599 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.989A pdb=" N ALA B 634 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B 635 " --> pdb=" O HIS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 691 Processing helix chain 'B' and resid 704 through 723 removed outlier: 3.528A pdb=" N LEU B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 755 Processing helix chain 'B' and resid 762 through 773 Processing helix chain 'B' and resid 784 through 795 Processing helix chain 'B' and resid 797 through 802 Processing helix chain 'B' and resid 827 through 829 No H-bonds generated for 'chain 'B' and resid 827 through 829' Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 845 through 883 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) removed outlier: 3.722A pdb=" N ASN B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP B 875 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 876 " --> pdb=" O GLU B 872 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 883 " --> pdb=" O GLN B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 896 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 900 through 929 removed outlier: 4.021A pdb=" N LEU B 904 " --> pdb=" O VAL B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 944 Processing helix chain 'B' and resid 952 through 964 Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 989 through 1012 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) Proline residue: B1008 - end of helix removed outlier: 4.655A pdb=" N ALA B1011 " --> pdb=" O LEU B1007 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER B1012 " --> pdb=" O PRO B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1030 through 1046 removed outlier: 3.862A pdb=" N ALA B1033 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B1038 " --> pdb=" O ALA B1035 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B1044 " --> pdb=" O ALA B1041 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B1045 " --> pdb=" O ALA B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1071 Processing helix chain 'B' and resid 1081 through 1094 Processing helix chain 'B' and resid 1100 through 1106 Processing helix chain 'B' and resid 1109 through 1120 Processing helix chain 'C' and resid 25 through 82 removed outlier: 4.066A pdb=" N ILE C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'D' and resid 11 through 68 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 12 through 39 Processing helix chain 'E' and resid 43 through 112 removed outlier: 4.497A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 24 Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.553A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Proline residue: F 69 - end of helix Processing helix chain 'F' and resid 87 through 95 removed outlier: 3.845A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.519A pdb=" N HIS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 120 No H-bonds generated for 'chain 'F' and resid 117 through 120' Processing helix chain 'F' and resid 123 through 131 Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'F' and resid 165 through 176 removed outlier: 3.857A pdb=" N PHE F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 25 Processing helix chain 'G' and resid 69 through 71 No H-bonds generated for 'chain 'G' and resid 69 through 71' Processing helix chain 'G' and resid 87 through 95 removed outlier: 3.933A pdb=" N ARG G 94 " --> pdb=" O PHE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 123 through 131 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 165 through 177 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) Processing sheet with id= A, first strand: chain 'A' and resid 304 through 306 Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 855 through 858 Processing sheet with id= D, first strand: chain 'B' and resid 695 through 697 Processing sheet with id= E, 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= F, first strand: chain 'F' and resid 153 through 156 removed outlier: 4.262A pdb=" N LYS F 153 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE F 4 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN F 52 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS F 6 " --> pdb=" O ASN F 52 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY F 54 " --> pdb=" O CYS F 6 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL F 8 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TRP F 56 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N GLY F 10 " --> pdb=" O TRP F 56 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 109 through 115 removed outlier: 3.673A pdb=" N VAL G 7 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE G 4 " --> pdb=" O PRO G 50 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN G 52 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS G 6 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY G 54 " --> pdb=" O CYS G 6 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL G 8 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP G 56 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLY G 10 " --> pdb=" O TRP G 56 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR G 58 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP G 38 " --> pdb=" O ASP G 57 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 3675 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: 8.10 Time building geometry restraints manager: 11.11 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: 99.91 - 106.99: 686 106.99 - 114.06: 13997 114.06 - 121.14: 12507 121.14 - 128.21: 5591 128.21 - 135.28: 192 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: 52 2.45 - 3.06: 16531 3.06 - 3.68: 35960 3.68 - 4.29: 51444 4.29 - 4.90: 86962 Nonbonded interactions: 190949 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 2.520 nonbonded pdb=" O1B GTP G 500 " pdb="MG MG G 501 " model vdw 2.198 2.170 ... (remaining 190944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.510 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: 5.010 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 65.530 Find NCS groups from input model: 1.100 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: 0.000 Load rotamer database and sin/cos tables:14.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.860 ------------------------------------------------------------------------------- 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= 0.330 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 673 time to evaluate : 2.864 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: 1.5841 time to fit residues: 1202.7984 Evaluate side-chains 542 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 537 time to evaluate : 3.117 ------------------------------------------------------------------------------- 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: 3.9990 chunk 221 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 A 637 GLN A 830 HIS A 831 ASN A1030 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 448 ASN B 555 GLN B1114 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24382 Z= 0.316 Angle : 0.650 9.683 32973 Z= 0.336 Chirality : 0.043 0.167 3738 Planarity : 0.005 0.049 4188 Dihedral : 6.574 148.925 3280 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.85 % Allowed : 13.03 % Favored : 84.12 % 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: 2.43 (0.16), residues: 2920 helix: 2.35 (0.12), residues: 1932 sheet: 1.86 (0.51), residues: 107 loop : -0.07 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 97 HIS 0.006 0.001 HIS A1128 PHE 0.018 0.002 PHE A 844 TYR 0.030 0.002 TYR B 140 ARG 0.008 0.001 ARG A1034 *********************** 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 615 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 539 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.7179 (ttp80) REVERT: A 69 MET cc_start: 0.7881 (mmm) cc_final: 0.7307 (mmm) REVERT: A 74 GLU cc_start: 0.7807 (pp20) cc_final: 0.7060 (pp20) REVERT: A 614 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: A 807 MET cc_start: 0.7859 (tpp) cc_final: 0.7542 (ttp) REVERT: A 964 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7671 (mtt-85) REVERT: B 27 MET cc_start: 0.7780 (mpm) cc_final: 0.7466 (mpm) REVERT: B 122 ASP cc_start: 0.7177 (t0) cc_final: 0.6919 (t0) REVERT: B 211 GLN cc_start: 0.7326 (tp40) cc_final: 0.7123 (tp-100) REVERT: B 228 GLN cc_start: 0.7605 (mt0) cc_final: 0.6934 (mt0) REVERT: B 254 SER cc_start: 0.7899 (t) cc_final: 0.7364 (t) REVERT: B 392 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6982 (tmm) REVERT: B 510 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6600 (mtp85) REVERT: B 626 ASP cc_start: 0.7679 (t0) cc_final: 0.7394 (t0) REVERT: B 666 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (mtp85) REVERT: B 725 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7481 (mpp) REVERT: F 119 LEU cc_start: 0.8263 (mt) cc_final: 0.8048 (mm) REVERT: G 26 ASN cc_start: 0.8110 (t0) cc_final: 0.7854 (t0) REVERT: G 63 ASP cc_start: 0.7115 (p0) cc_final: 0.6686 (p0) outliers start: 76 outliers final: 22 residues processed: 572 average time/residue: 1.6893 time to fit residues: 1080.5289 Evaluate side-chains 538 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 510 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 486 ASP Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 246 ASP 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 582 GLU Chi-restraints excluded: chain B residue 666 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 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 68 LEU Chi-restraints excluded: chain E residue 147 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 213 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 407 HIS A 614 GLN A 831 ASN A1030 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 766 ASN B 826 ASN C 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2978 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= 0.185 Angle : 0.584 10.295 32973 Z= 0.299 Chirality : 0.038 0.150 3738 Planarity : 0.004 0.047 4188 Dihedral : 6.284 149.515 3273 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.55 % Allowed : 17.04 % Favored : 80.41 % 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: 2.28 (0.16), residues: 2920 helix: 2.21 (0.12), residues: 1928 sheet: 1.68 (0.50), residues: 109 loop : -0.04 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 97 HIS 0.005 0.001 HIS A1058 PHE 0.018 0.001 PHE B 410 TYR 0.022 0.001 TYR B 930 ARG 0.009 0.001 ARG A1034 *********************** 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 599 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 531 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7182 (ttp-170) cc_final: 0.6931 (ttp80) REVERT: A 69 MET cc_start: 0.7838 (mmm) cc_final: 0.7272 (mmm) REVERT: A 81 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8775 (t) REVERT: A 212 MET cc_start: 0.7432 (mmt) cc_final: 0.7217 (mmt) REVERT: A 650 ASP cc_start: 0.7069 (t70) cc_final: 0.6797 (t0) REVERT: A 807 MET cc_start: 0.7792 (tpp) cc_final: 0.7543 (ttp) REVERT: A 964 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7064 (mtt-85) REVERT: B 78 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7091 (tm-30) REVERT: B 122 ASP cc_start: 0.7074 (t0) cc_final: 0.6852 (t0) REVERT: B 228 GLN cc_start: 0.7618 (mt0) cc_final: 0.6657 (mt0) REVERT: B 392 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6999 (tmm) REVERT: B 510 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6574 (mtp85) REVERT: B 626 ASP cc_start: 0.7559 (t0) cc_final: 0.7239 (t0) REVERT: B 725 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7676 (mtm) REVERT: B 856 MET cc_start: 0.7037 (mmp) cc_final: 0.6819 (mmp) REVERT: C 70 GLN cc_start: 0.8506 (tp40) cc_final: 0.7994 (tp40) REVERT: F 115 THR cc_start: 0.8783 (m) cc_final: 0.8547 (p) REVERT: G 26 ASN cc_start: 0.8090 (t0) cc_final: 0.7826 (t0) REVERT: G 63 ASP cc_start: 0.7088 (p0) cc_final: 0.6667 (p0) REVERT: G 156 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6513 (mm-30) outliers start: 68 outliers final: 27 residues processed: 560 average time/residue: 1.6069 time to fit residues: 1009.5758 Evaluate side-chains 540 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 508 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 81 VAL 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 444 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 246 ASP 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 D residue 47 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 133 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 262 optimal weight: 20.0000 chunk 199 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 178 optimal weight: 0.4980 chunk 266 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 348 GLN A 407 HIS A 596 HIS A1030 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 766 ASN C 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24382 Z= 0.182 Angle : 0.599 9.629 32973 Z= 0.303 Chirality : 0.038 0.144 3738 Planarity : 0.004 0.046 4188 Dihedral : 6.283 149.861 3273 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.18 % Allowed : 18.73 % Favored : 79.09 % 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: 2.20 (0.16), residues: 2920 helix: 2.14 (0.12), residues: 1925 sheet: 1.44 (0.48), residues: 109 loop : -0.01 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 97 HIS 0.004 0.001 HIS A 651 PHE 0.025 0.001 PHE B 410 TYR 0.024 0.001 TYR B 930 ARG 0.008 0.001 ARG G 174 *********************** 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 586 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 528 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7873 (mmm) cc_final: 0.7312 (mmm) REVERT: A 75 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 81 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8726 (t) REVERT: A 348 GLN cc_start: 0.7324 (mt0) cc_final: 0.7099 (mt0) REVERT: A 650 ASP cc_start: 0.7085 (t70) cc_final: 0.6849 (t0) REVERT: A 964 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6784 (mtt-85) REVERT: A 1204 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6620 (ttt) REVERT: B 78 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7079 (tm-30) REVERT: B 122 ASP cc_start: 0.6985 (t0) cc_final: 0.6726 (t0) REVERT: B 228 GLN cc_start: 0.7531 (mt0) cc_final: 0.6493 (mt0) REVERT: B 510 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6552 (mtp85) REVERT: B 626 ASP cc_start: 0.7522 (t0) cc_final: 0.7179 (t0) REVERT: B 725 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7496 (mtm) REVERT: F 115 THR cc_start: 0.8765 (m) cc_final: 0.8520 (p) REVERT: G 63 ASP cc_start: 0.7130 (p0) cc_final: 0.6703 (p0) REVERT: G 94 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8500 (ttp80) outliers start: 58 outliers final: 23 residues processed: 551 average time/residue: 1.6508 time to fit residues: 1020.4972 Evaluate side-chains 535 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 507 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 246 ASP 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 C residue 74 ASP Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 133 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 253 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN A 351 GLN A 596 HIS ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS B 766 ASN C 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24382 Z= 0.240 Angle : 0.622 9.928 32973 Z= 0.316 Chirality : 0.040 0.153 3738 Planarity : 0.004 0.050 4188 Dihedral : 6.301 150.525 3273 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.63 % Allowed : 20.68 % Favored : 76.69 % 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: 2.04 (0.16), residues: 2920 helix: 2.03 (0.12), residues: 1926 sheet: 1.33 (0.47), residues: 109 loop : -0.12 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.008 0.001 HIS A1058 PHE 0.023 0.001 PHE B 410 TYR 0.025 0.001 TYR B 930 ARG 0.010 0.001 ARG G 174 *********************** 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 588 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 518 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7067 (ttp-170) cc_final: 0.6860 (ttp80) REVERT: A 69 MET cc_start: 0.7905 (mmm) cc_final: 0.7352 (mmm) REVERT: A 81 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (t) REVERT: A 148 ARG cc_start: 0.6745 (tpp80) cc_final: 0.6440 (ttm-80) REVERT: A 650 ASP cc_start: 0.7209 (t70) cc_final: 0.6939 (t0) REVERT: A 807 MET cc_start: 0.7808 (tpp) cc_final: 0.7581 (ttp) REVERT: A 1204 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6770 (ttt) REVERT: B 78 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7148 (tm-30) REVERT: B 122 ASP cc_start: 0.7012 (t0) cc_final: 0.6781 (t0) REVERT: B 258 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6800 (mpp) REVERT: B 510 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6621 (mtp85) REVERT: B 626 ASP cc_start: 0.7514 (t0) cc_final: 0.7164 (t0) REVERT: B 725 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: D 47 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7830 (mp) REVERT: F 115 THR cc_start: 0.8824 (m) cc_final: 0.8513 (p) REVERT: G 63 ASP cc_start: 0.7162 (p0) cc_final: 0.6767 (p0) REVERT: G 170 ASP cc_start: 0.7667 (t70) cc_final: 0.7281 (t0) outliers start: 70 outliers final: 31 residues processed: 552 average time/residue: 1.6570 time to fit residues: 1035.2719 Evaluate side-chains 546 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 509 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER 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 444 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1204 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 246 ASP Chi-restraints excluded: chain B residue 258 MET 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 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 68 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 96 LYS 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 133 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 282 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 280 ASN A 596 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 766 ASN B 873 ASN F 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24382 Z= 0.362 Angle : 0.695 8.922 32973 Z= 0.353 Chirality : 0.043 0.161 3738 Planarity : 0.005 0.055 4188 Dihedral : 6.442 152.178 3273 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.97 % Allowed : 21.36 % Favored : 75.68 % 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: 1.74 (0.16), residues: 2920 helix: 1.81 (0.12), residues: 1906 sheet: 1.28 (0.47), residues: 109 loop : -0.21 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 97 HIS 0.007 0.001 HIS A1058 PHE 0.025 0.002 PHE B 410 TYR 0.028 0.002 TYR B 930 ARG 0.012 0.001 ARG G 174 *********************** 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 606 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 527 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7963 (mmm) cc_final: 0.7430 (mmm) REVERT: A 148 ARG cc_start: 0.6815 (tpp80) cc_final: 0.6539 (ttm-80) REVERT: A 274 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7359 (mmm) REVERT: A 473 ASN cc_start: 0.7808 (m-40) cc_final: 0.7595 (m110) REVERT: A 650 ASP cc_start: 0.7400 (t70) cc_final: 0.7149 (t0) REVERT: A 807 MET cc_start: 0.7972 (tpp) cc_final: 0.7382 (ttp) REVERT: A 964 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: A 1051 GLU cc_start: 0.7542 (pp20) cc_final: 0.7202 (pp20) REVERT: A 1204 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6869 (ttt) REVERT: B 78 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7249 (tm-30) REVERT: B 228 GLN cc_start: 0.7598 (mt0) cc_final: 0.7164 (mt0) REVERT: B 258 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.6927 (mpp) REVERT: B 626 ASP cc_start: 0.7586 (t0) cc_final: 0.7240 (t0) REVERT: B 691 TYR cc_start: 0.7411 (t80) cc_final: 0.7112 (t80) REVERT: B 725 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7378 (mpp) REVERT: D 47 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7907 (mp) REVERT: F 154 TYR cc_start: 0.7265 (t80) cc_final: 0.7046 (t80) REVERT: G 63 ASP cc_start: 0.7161 (p0) cc_final: 0.6817 (p0) REVERT: G 170 ASP cc_start: 0.7696 (t70) cc_final: 0.7389 (t0) outliers start: 79 outliers final: 36 residues processed: 568 average time/residue: 1.6441 time to fit residues: 1046.8150 Evaluate side-chains 558 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 516 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 725 MET 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 C residue 97 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 133 LYS Chi-restraints excluded: chain G residue 135 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 159 optimal weight: 0.0970 chunk 237 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- 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** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN B 826 ASN B 873 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24382 Z= 0.215 Angle : 0.677 9.124 32973 Z= 0.340 Chirality : 0.040 0.137 3738 Planarity : 0.004 0.050 4188 Dihedral : 6.377 152.847 3271 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.40 % Allowed : 23.42 % Favored : 74.17 % 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: 1.85 (0.16), residues: 2920 helix: 1.92 (0.12), residues: 1905 sheet: 1.32 (0.47), residues: 109 loop : -0.22 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 97 HIS 0.006 0.001 HIS A1058 PHE 0.030 0.001 PHE B 410 TYR 0.026 0.001 TYR B 930 ARG 0.012 0.001 ARG G 174 *********************** 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 593 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 529 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7864 (mmm) cc_final: 0.7354 (mmm) REVERT: A 81 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8758 (t) REVERT: A 274 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: A 300 LYS cc_start: 0.8794 (tppp) cc_final: 0.8452 (tppp) REVERT: A 807 MET cc_start: 0.7858 (tpp) cc_final: 0.7476 (ttp) REVERT: A 930 MET cc_start: 0.7611 (mmm) cc_final: 0.7357 (mmp) REVERT: A 964 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7391 (mtt-85) REVERT: B 78 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7200 (tm-30) REVERT: B 228 GLN cc_start: 0.7561 (mt0) cc_final: 0.6696 (mt0) REVERT: B 258 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.6811 (mpp) REVERT: B 626 ASP cc_start: 0.7530 (t0) cc_final: 0.7187 (t0) REVERT: F 115 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8553 (p) REVERT: G 63 ASP cc_start: 0.7140 (p0) cc_final: 0.6791 (p0) REVERT: G 170 ASP cc_start: 0.7663 (t70) cc_final: 0.7403 (t0) outliers start: 64 outliers final: 31 residues processed: 558 average time/residue: 1.6353 time to fit residues: 1025.7858 Evaluate side-chains 560 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 524 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 885 ASP 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 68 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 115 THR 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 135 THR Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 178 optimal weight: 0.0980 chunk 191 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 A 280 ASN A 473 ASN A1029 GLN B 11 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN B 873 ASN C 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4074 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= 0.208 Angle : 0.693 10.930 32973 Z= 0.346 Chirality : 0.039 0.222 3738 Planarity : 0.005 0.058 4188 Dihedral : 6.261 152.742 3267 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.88 % Allowed : 24.74 % Favored : 73.39 % 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: 1.90 (0.16), residues: 2920 helix: 1.97 (0.12), residues: 1897 sheet: 1.18 (0.45), residues: 114 loop : -0.21 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 97 HIS 0.007 0.001 HIS A1058 PHE 0.034 0.001 PHE B 410 TYR 0.026 0.001 TYR B 930 ARG 0.014 0.001 ARG B 547 *********************** 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 577 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 527 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7840 (mmm) cc_final: 0.7375 (mmm) REVERT: A 274 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7321 (mmm) REVERT: A 751 LYS cc_start: 0.8303 (ptpp) cc_final: 0.8094 (mtmm) REVERT: A 807 MET cc_start: 0.7889 (tpp) cc_final: 0.7464 (ttp) REVERT: A 964 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7753 (mtt-85) REVERT: B 78 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7216 (tm-30) REVERT: B 228 GLN cc_start: 0.7510 (mt0) cc_final: 0.7048 (mt0) REVERT: B 626 ASP cc_start: 0.7503 (t0) cc_final: 0.7154 (t0) REVERT: G 63 ASP cc_start: 0.7126 (p0) cc_final: 0.6772 (p0) REVERT: G 130 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6629 (ttpp) REVERT: G 170 ASP cc_start: 0.7560 (t70) cc_final: 0.7296 (t0) outliers start: 50 outliers final: 30 residues processed: 549 average time/residue: 1.6095 time to fit residues: 991.4104 Evaluate side-chains 547 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 514 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 803 GLU Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 757 VAL 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 129 ASN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 115 THR 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 133 LYS Chi-restraints excluded: chain G residue 135 THR 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 256 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 262 optimal weight: 30.0000 chunk 157 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 236 optimal weight: 9.9990 chunk 248 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 280 ASN A 596 HIS B 11 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24382 Z= 0.241 Angle : 0.739 11.838 32973 Z= 0.367 Chirality : 0.040 0.228 3738 Planarity : 0.005 0.056 4188 Dihedral : 6.228 152.838 3267 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.06 % Allowed : 25.23 % Favored : 72.71 % 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: 1.86 (0.16), residues: 2920 helix: 1.97 (0.12), residues: 1895 sheet: 1.03 (0.47), residues: 119 loop : -0.28 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 86 HIS 0.005 0.001 HIS A1058 PHE 0.033 0.001 PHE B 410 TYR 0.027 0.001 TYR F 154 ARG 0.014 0.001 ARG G 174 *********************** 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 577 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 522 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7848 (mmm) cc_final: 0.7409 (mmm) REVERT: A 75 GLU cc_start: 0.7837 (tp30) cc_final: 0.7604 (tp30) REVERT: A 274 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7341 (mmm) REVERT: A 300 LYS cc_start: 0.8796 (tppp) cc_final: 0.8504 (tppp) REVERT: A 310 ASP cc_start: 0.7437 (t0) cc_final: 0.7198 (t0) REVERT: A 751 LYS cc_start: 0.8283 (ptpp) cc_final: 0.8077 (mtmm) REVERT: A 807 MET cc_start: 0.7929 (tpp) cc_final: 0.7251 (ttp) REVERT: A 964 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7664 (mtt-85) REVERT: B 78 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7243 (tm-30) REVERT: B 228 GLN cc_start: 0.7514 (mt0) cc_final: 0.7028 (mt0) REVERT: B 258 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.6462 (mpp) REVERT: B 626 ASP cc_start: 0.7511 (t0) cc_final: 0.7301 (t0) REVERT: B 731 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: F 156 GLU cc_start: 0.7438 (mp0) cc_final: 0.6812 (mp0) REVERT: G 63 ASP cc_start: 0.7117 (p0) cc_final: 0.6768 (p0) REVERT: G 130 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6936 (ttpp) REVERT: G 170 ASP cc_start: 0.7592 (t70) cc_final: 0.7335 (t0) outliers start: 55 outliers final: 32 residues processed: 543 average time/residue: 1.6460 time to fit residues: 1007.3237 Evaluate side-chains 544 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 507 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 597 ARG 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 964 ARG Chi-restraints excluded: chain A residue 1068 THR 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 258 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 930 TYR 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 68 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 115 THR 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 133 LYS Chi-restraints excluded: chain G residue 135 THR 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 172 optimal weight: 0.4980 chunk 277 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 231 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 596 HIS B 11 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN B 873 ASN C 70 GLN F 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24382 Z= 0.214 Angle : 0.748 12.519 32973 Z= 0.373 Chirality : 0.039 0.199 3738 Planarity : 0.005 0.072 4188 Dihedral : 6.201 152.579 3267 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.35 % Allowed : 26.09 % Favored : 72.56 % 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: 1.87 (0.16), residues: 2920 helix: 1.97 (0.12), residues: 1901 sheet: 0.98 (0.47), residues: 119 loop : -0.28 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 86 HIS 0.005 0.001 HIS A1058 PHE 0.043 0.001 PHE B 410 TYR 0.028 0.001 TYR F 154 ARG 0.014 0.001 ARG G 174 ********************** 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 554 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 518 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7808 (mmm) cc_final: 0.7357 (mmm) REVERT: A 274 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7343 (mmm) REVERT: A 310 ASP cc_start: 0.7363 (t0) cc_final: 0.7128 (t0) REVERT: A 807 MET cc_start: 0.7884 (tpp) cc_final: 0.7544 (ttp) REVERT: B 78 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7225 (tm-30) REVERT: B 444 GLU cc_start: 0.6866 (pp20) cc_final: 0.6650 (pp20) REVERT: B 731 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: F 115 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8523 (p) REVERT: F 154 TYR cc_start: 0.6487 (t80) cc_final: 0.6253 (t80) REVERT: F 156 GLU cc_start: 0.7404 (mp0) cc_final: 0.6838 (mp0) REVERT: G 63 ASP cc_start: 0.7127 (p0) cc_final: 0.6761 (p0) REVERT: G 130 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6764 (ttpp) REVERT: G 170 ASP cc_start: 0.7581 (t70) cc_final: 0.7317 (t0) outliers start: 36 outliers final: 24 residues processed: 533 average time/residue: 1.5855 time to fit residues: 951.7316 Evaluate side-chains 531 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 503 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 753 ILE 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 129 ASN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 115 THR 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 133 LYS Chi-restraints excluded: chain G residue 135 THR 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 184 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 280 ASN ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN B 873 ASN F 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100843 restraints weight = 49472.618| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.74 r_work: 0.3340 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24382 Z= 0.241 Angle : 0.767 12.645 32973 Z= 0.382 Chirality : 0.040 0.202 3738 Planarity : 0.005 0.060 4188 Dihedral : 6.198 152.198 3267 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.50 % Allowed : 26.50 % Favored : 72.00 % 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: 1.83 (0.16), residues: 2920 helix: 1.96 (0.12), residues: 1899 sheet: 0.86 (0.45), residues: 124 loop : -0.31 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 86 HIS 0.004 0.001 HIS A1128 PHE 0.028 0.001 PHE G 28 TYR 0.054 0.001 TYR B 565 ARG 0.014 0.001 ARG G 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13736.62 seconds wall clock time: 242 minutes 51.74 seconds (14571.74 seconds total)