Starting phenix.real_space_refine on Tue Jul 23 21:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/07_2024/7use_26734_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/07_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_26734/07_2024/7use_26734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/07_2024/7use_26734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/07_2024/7use_26734_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7use_26734/07_2024/7use_26734_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 161 5.16 5 C 15230 2.51 5 N 4067 2.21 5 O 4447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 12.35, per 1000 atoms: 0.52 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: 8.96 Conformation dependent library (CDL) restraints added in 4.1 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 9 sheets defined 74.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.744A pdb=" N LEU A 17 " --> pdb=" O ASN A 13 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 85 removed outlier: 3.688A pdb=" N GLN A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 116 through 144 removed outlier: 3.528A pdb=" N THR A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 removed outlier: 4.259A pdb=" N LYS A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 removed outlier: 3.505A pdb=" N LEU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 230 removed outlier: 4.043A pdb=" N VAL A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.701A pdb=" N LEU A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 3.670A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 302 removed outlier: 4.361A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 4.179A pdb=" N ILE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 4.468A pdb=" N GLU A 326 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 327 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 329 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 365 removed outlier: 3.774A pdb=" N ILE A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.569A pdb=" N TYR A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 444 through 468 Processing helix chain 'A' and resid 468 through 490 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'A' and resid 504 through 518 removed outlier: 3.585A pdb=" N VAL A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.665A pdb=" N ARG A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.851A pdb=" N ILE A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.504A pdb=" N SER A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.866A pdb=" N ILE A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.594A pdb=" N ASN A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.954A pdb=" N LEU A 621 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP A 622 " --> pdb=" O SER A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 622' Processing helix chain 'A' and resid 624 through 630 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 669 through 681 removed outlier: 3.564A pdb=" N ASP A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 723 removed outlier: 3.613A pdb=" N LEU A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.627A pdb=" N ARG A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 752 removed outlier: 4.643A pdb=" N LEU A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 789 removed outlier: 3.603A pdb=" N LEU A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 removed outlier: 6.183A pdb=" N THR A 793 " --> pdb=" O GLU A 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 794 through 814 Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 837 through 850 removed outlier: 3.555A pdb=" N LEU A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 903 removed outlier: 3.509A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 910 through 922 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 943 through 955 removed outlier: 3.513A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 955 " --> pdb=" O THR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 967 Processing helix chain 'A' and resid 968 through 980 removed outlier: 3.661A pdb=" N GLU A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 986 Processing helix chain 'A' and resid 987 through 991 Processing helix chain 'A' and resid 992 through 1025 removed outlier: 3.599A pdb=" N HIS A1024 " --> pdb=" O CYS A1020 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 removed outlier: 3.882A pdb=" N ASN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1055 through 1058 Processing helix chain 'A' and resid 1059 through 1066 Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1092 through 1104 Processing helix chain 'A' and resid 1106 through 1110 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.622A pdb=" N LEU A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1155 through 1168 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1200 through 1226 removed outlier: 3.652A pdb=" N MET A1204 " --> pdb=" O PRO A1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 12 through 40 removed outlier: 3.565A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.909A pdb=" N ILE B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.557A pdb=" N LYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.822A pdb=" N GLN B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 81' Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.551A pdb=" N ILE B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 118 Processing helix chain 'B' and resid 126 through 150 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.591A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.753A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.502A pdb=" N GLU B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 270 through 276 removed outlier: 4.220A pdb=" N ASN B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.575A pdb=" N SER B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 313 removed outlier: 4.314A pdb=" N ASN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 360 removed outlier: 5.481A pdb=" N GLY B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.822A pdb=" N GLY B 365 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 391 removed outlier: 3.502A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 removed outlier: 3.827A pdb=" N LEU B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 437 removed outlier: 3.752A pdb=" N MET B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 453 through 470 removed outlier: 3.676A pdb=" N ILE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.869A pdb=" N GLU B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 477' Processing helix chain 'B' and resid 483 through 499 removed outlier: 3.672A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 508 No H-bonds generated for 'chain 'B' and resid 506 through 508' Processing helix chain 'B' and resid 509 through 528 Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.565A pdb=" N PHE B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 Processing helix chain 'B' and resid 560 through 566 removed outlier: 4.015A pdb=" N ARG B 564 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 574 through 580 removed outlier: 4.078A pdb=" N MET B 577 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 580 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 627 removed outlier: 4.495A pdb=" N HIS B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 removed outlier: 6.116A pdb=" N LYS B 631 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 673 through 692 removed outlier: 3.578A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 724 removed outlier: 3.934A pdb=" N TYR B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 724 " --> pdb=" O ILE B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 755 Processing helix chain 'B' and resid 761 through 774 Processing helix chain 'B' and resid 783 through 796 Processing helix chain 'B' and resid 796 through 803 Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 844 through 872 removed outlier: 3.587A pdb=" N LYS B 868 " --> pdb=" O ALA B 864 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 882 removed outlier: 3.791A pdb=" N THR B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.525A pdb=" N MET B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 930 removed outlier: 4.116A pdb=" N VAL B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 904 " --> pdb=" O VAL B 900 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.504A pdb=" N ALA B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 988 through 1007 removed outlier: 3.729A pdb=" N MET B1000 " --> pdb=" O ALA B 996 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B1001 " --> pdb=" O CYS B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1017 removed outlier: 5.822A pdb=" N VAL B1014 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET B1015 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B1017 " --> pdb=" O VAL B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1047 Processing helix chain 'B' and resid 1051 through 1072 removed outlier: 4.046A pdb=" N GLU B1072 " --> pdb=" O LYS B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.631A pdb=" N VAL B1084 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1107 removed outlier: 3.559A pdb=" N LEU B1103 " --> pdb=" O THR B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1121 removed outlier: 4.220A pdb=" N LEU B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 81 removed outlier: 4.066A pdb=" N ILE C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 83 No H-bonds generated for 'chain 'C' and resid 82 through 83' Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 128 removed outlier: 4.129A pdb=" N CYS C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'D' and resid 11 through 69 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 11 through 40 Processing helix chain 'E' and resid 42 through 111 removed outlier: 4.057A pdb=" N ALA E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 61 through 66 removed outlier: 4.553A pdb=" N ARG F 66 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 96 removed outlier: 3.565A pdb=" N PHE F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.519A pdb=" N HIS F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.978A pdb=" N ASP F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.643A pdb=" N GLY F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 3.857A pdb=" N PHE F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 Processing helix chain 'G' and resid 68 through 72 Processing helix chain 'G' and resid 86 through 96 removed outlier: 3.566A pdb=" N PHE G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG G 94 " --> pdb=" O PHE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.567A pdb=" N ILE G 126 " --> pdb=" O ASP G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.642A pdb=" N GLY G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 removed outlier: 3.817A pdb=" N VAL G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 306 Processing sheet with id=AA2, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.579A pdb=" N VAL A 755 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 855 through 858 Processing sheet with id=AA4, first strand: chain 'A' and resid 1090 through 1091 Processing sheet with id=AA5, first strand: chain 'B' and resid 292 through 296 removed outlier: 6.929A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 695 through 697 Processing sheet with id=AA7, first strand: chain 'B' and resid 805 through 808 removed outlier: 3.537A pdb=" N ALA B 806 " --> pdb=" O VAL B 815 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 46 removed outlier: 6.072A pdb=" N ILE F 4 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TRP F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 7 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE F 78 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS F 153 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 37 through 46 removed outlier: 3.544A pdb=" N ASP G 38 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR G 58 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY G 10 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 7 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE G 78 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL G 113 " --> pdb=" O PHE G 78 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 80 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR G 115 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE G 82 " --> pdb=" O THR G 115 " (cutoff:3.500A) 1539 hydrogen bonds defined for protein. 4467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 9.82 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: 51 2.45 - 3.06: 16369 3.06 - 3.68: 35899 3.68 - 4.29: 51089 4.29 - 4.90: 86865 Nonbonded interactions: 190273 Sorted by model distance: nonbonded pdb=" CG2 THR G 35 " pdb="MG MG G 501 " model vdw 1.840 2.590 nonbonded pdb=" O3G GTP G 500 " pdb="MG MG G 501 " model vdw 2.072 2.170 nonbonded pdb=" O PHE F 37 " pdb=" OD1 ASP F 38 " model vdw 2.163 3.040 nonbonded pdb=" NH1 ARG B 611 " pdb=" OD1 ASN B 612 " model vdw 2.184 2.520 nonbonded pdb=" O1B GTP G 500 " pdb="MG MG G 501 " model vdw 2.198 2.170 ... (remaining 190268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 59.310 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.440 ------------------------------------------------------------------------------- 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= 0.327 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 : 2.559 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: 1.5594 time to fit residues: 1184.2425 Evaluate side-chains 542 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 537 time to evaluate : 2.633 ------------------------------------------------------------------------------- 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: 2.9990 chunk 221 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 75 optimal weight: 0.0570 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 208 GLN A 473 ASN A 596 HIS A 614 GLN A1030 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 448 ASN B 555 GLN B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24382 Z= 0.259 Angle : 0.631 9.728 32973 Z= 0.326 Chirality : 0.041 0.171 3738 Planarity : 0.004 0.047 4188 Dihedral : 6.553 149.462 3280 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.63 % Allowed : 13.29 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.16), residues: 2920 helix: 2.74 (0.12), residues: 1954 sheet: 1.66 (0.50), residues: 109 loop : 0.03 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 97 HIS 0.006 0.001 HIS A1128 PHE 0.018 0.001 PHE A 600 TYR 0.029 0.001 TYR B 140 ARG 0.009 0.001 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 530 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.7105 (ttp80) REVERT: A 69 MET cc_start: 0.7878 (mmm) cc_final: 0.7293 (mmm) REVERT: A 74 GLU cc_start: 0.7801 (pp20) cc_final: 0.7186 (pp20) REVERT: A 357 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6326 (ttp) REVERT: A 650 ASP cc_start: 0.6982 (t70) cc_final: 0.6666 (OUTLIER) REVERT: A 1204 MET cc_start: 0.6960 (ttt) cc_final: 0.6672 (ttt) REVERT: B 122 ASP cc_start: 0.7095 (t0) cc_final: 0.6765 (t0) REVERT: B 211 GLN cc_start: 0.7133 (tp40) cc_final: 0.6895 (tp-100) REVERT: B 392 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6992 (tmm) REVERT: B 510 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.5995 (mtp85) REVERT: B 725 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7428 (mpp) REVERT: B 951 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.6112 (t0) REVERT: F 119 LEU cc_start: 0.8221 (mt) cc_final: 0.7941 (mm) REVERT: G 63 ASP cc_start: 0.7095 (p0) cc_final: 0.6673 (p0) outliers start: 70 outliers final: 20 residues processed: 558 average time/residue: 1.5767 time to fit residues: 989.0553 Evaluate side-chains 527 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 503 time to evaluate : 2.709 ------------------------------------------------------------------------------- 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 357 MET Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain B residue 68 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 B residue 773 THR Chi-restraints excluded: chain B residue 951 ASP 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 147 ASP Chi-restraints excluded: chain G residue 118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 265 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 596 HIS ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24382 Z= 0.285 Angle : 0.627 10.078 32973 Z= 0.323 Chirality : 0.042 0.161 3738 Planarity : 0.004 0.053 4188 Dihedral : 6.336 149.600 3273 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.23 % Allowed : 15.62 % Favored : 81.16 % 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: 2.53 (0.16), residues: 2920 helix: 2.46 (0.12), residues: 1942 sheet: 1.66 (0.50), residues: 109 loop : -0.14 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.011 0.001 HIS A1058 PHE 0.021 0.002 PHE A 600 TYR 0.027 0.001 TYR B 140 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 613 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 527 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.7118 (ttp80) REVERT: A 69 MET cc_start: 0.7873 (mmm) cc_final: 0.7285 (mmm) REVERT: A 74 GLU cc_start: 0.7773 (pp20) cc_final: 0.7534 (pp20) REVERT: A 114 VAL cc_start: 0.8822 (t) cc_final: 0.8582 (p) REVERT: A 148 ARG cc_start: 0.6889 (tpp80) cc_final: 0.6676 (ttm-80) REVERT: A 206 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 274 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7317 (mtm) REVERT: A 310 ASP cc_start: 0.7654 (t0) cc_final: 0.7445 (t0) REVERT: A 650 ASP cc_start: 0.7192 (t70) cc_final: 0.5828 (t0) REVERT: A 654 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: A 786 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7157 (ttm170) REVERT: A 964 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7556 (mtt-85) REVERT: A 1204 MET cc_start: 0.6991 (ttt) cc_final: 0.6703 (ttt) REVERT: B 78 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7135 (tm-30) REVERT: B 151 GLU cc_start: 0.6440 (tp30) cc_final: 0.6162 (tm-30) REVERT: B 392 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7006 (tmm) REVERT: B 725 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7541 (mpp) REVERT: E 113 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8434 (p) REVERT: F 119 LEU cc_start: 0.8226 (mt) cc_final: 0.7971 (mm) REVERT: G 63 ASP cc_start: 0.7138 (p0) cc_final: 0.6787 (p0) outliers start: 86 outliers final: 32 residues processed: 563 average time/residue: 1.5698 time to fit residues: 992.5900 Evaluate side-chains 543 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 504 time to evaluate : 2.602 ------------------------------------------------------------------------------- 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 274 MET 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 597 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 786 ARG 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 63 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 1031 CYS Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 266 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 139 optimal weight: 0.0670 chunk 252 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 324 HIS ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24382 Z= 0.190 Angle : 0.613 9.583 32973 Z= 0.311 Chirality : 0.039 0.154 3738 Planarity : 0.004 0.050 4188 Dihedral : 6.270 149.909 3273 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.40 % Allowed : 19.11 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.16), residues: 2920 helix: 2.51 (0.12), residues: 1948 sheet: 1.50 (0.48), residues: 109 loop : -0.19 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 97 HIS 0.005 0.001 HIS B 509 PHE 0.017 0.001 PHE B 410 TYR 0.024 0.001 TYR B 930 ARG 0.010 0.001 ARG A1034 *********************** 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 581 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 517 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7856 (mmm) cc_final: 0.7307 (mmm) REVERT: A 75 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 114 VAL cc_start: 0.8786 (t) cc_final: 0.8506 (p) REVERT: A 310 ASP cc_start: 0.7632 (t0) cc_final: 0.7326 (t0) REVERT: A 650 ASP cc_start: 0.7109 (t70) cc_final: 0.5785 (t0) REVERT: A 654 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: A 964 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7551 (mtt-85) REVERT: A 1051 GLU cc_start: 0.7472 (pp20) cc_final: 0.7248 (pp20) REVERT: B 78 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7110 (tm-30) REVERT: B 258 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6918 (mmm) REVERT: B 510 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.5921 (mtp85) REVERT: B 725 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7681 (mtm) REVERT: G 63 ASP cc_start: 0.7135 (p0) cc_final: 0.6769 (p0) outliers start: 64 outliers final: 25 residues processed: 547 average time/residue: 1.5884 time to fit residues: 980.7063 Evaluate side-chains 536 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 506 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 107 ILE 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 486 ASP Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 654 GLU 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 1206 GLU Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 258 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 64 ILE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 253 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24382 Z= 0.194 Angle : 0.629 9.916 32973 Z= 0.317 Chirality : 0.039 0.245 3738 Planarity : 0.004 0.048 4188 Dihedral : 6.245 149.970 3273 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.52 % Allowed : 20.76 % Favored : 76.73 % 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: 2.58 (0.16), residues: 2920 helix: 2.54 (0.12), residues: 1942 sheet: 1.39 (0.48), residues: 109 loop : -0.17 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 97 HIS 0.004 0.001 HIS A1058 PHE 0.044 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 592 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 525 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7846 (mmm) cc_final: 0.7306 (mmm) REVERT: A 114 VAL cc_start: 0.8779 (t) cc_final: 0.8506 (p) REVERT: A 148 ARG cc_start: 0.6699 (tpp80) cc_final: 0.6392 (ttm-80) REVERT: A 166 ASN cc_start: 0.7506 (t0) cc_final: 0.7248 (t0) REVERT: A 310 ASP cc_start: 0.7613 (t0) cc_final: 0.7396 (t0) REVERT: A 650 ASP cc_start: 0.7108 (t70) cc_final: 0.6868 (t0) REVERT: A 930 MET cc_start: 0.7473 (mmp) cc_final: 0.7229 (mmp) REVERT: A 964 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7510 (mtt-85) REVERT: B 78 GLN cc_start: 0.7400 (mm-40) cc_final: 0.7096 (tm-30) REVERT: B 510 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.5884 (mtp85) REVERT: B 725 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.6961 (mtm) REVERT: G 63 ASP cc_start: 0.7142 (p0) cc_final: 0.6778 (p0) outliers start: 67 outliers final: 26 residues processed: 560 average time/residue: 1.5374 time to fit residues: 970.7847 Evaluate side-chains 529 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 500 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER 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 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 762 ILE 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 246 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 1031 CYS Chi-restraints excluded: chain C residue 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 32 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 218 ASN A1029 GLN A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 873 ASN C 70 GLN F 43 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24382 Z= 0.330 Angle : 0.703 11.517 32973 Z= 0.356 Chirality : 0.043 0.329 3738 Planarity : 0.004 0.052 4188 Dihedral : 6.307 151.073 3273 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.89 % Allowed : 21.51 % Favored : 75.60 % 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: 2.23 (0.16), residues: 2920 helix: 2.28 (0.12), residues: 1948 sheet: 1.34 (0.48), residues: 109 loop : -0.37 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 97 HIS 0.005 0.001 HIS A1128 PHE 0.022 0.002 PHE G 28 TYR 0.035 0.002 TYR E 32 ARG 0.011 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 609 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 532 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7935 (mmm) cc_final: 0.7403 (mmm) REVERT: A 114 VAL cc_start: 0.8767 (t) cc_final: 0.8480 (p) REVERT: A 148 ARG cc_start: 0.6909 (tpp80) cc_final: 0.6627 (ttm-80) REVERT: A 310 ASP cc_start: 0.7643 (t0) cc_final: 0.7257 (t0) REVERT: A 650 ASP cc_start: 0.7330 (t70) cc_final: 0.7114 (t0) REVERT: A 964 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7327 (mtt-85) REVERT: A 1051 GLU cc_start: 0.7552 (pp20) cc_final: 0.7258 (pp20) REVERT: B 78 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7301 (tm-30) REVERT: B 258 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.6959 (mmm) REVERT: B 405 ILE cc_start: 0.8267 (pp) cc_final: 0.7969 (mm) REVERT: B 510 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6226 (mtp85) REVERT: B 725 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7558 (mtm) REVERT: D 47 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7903 (mp) REVERT: G 63 ASP cc_start: 0.7147 (p0) cc_final: 0.6794 (p0) outliers start: 77 outliers final: 36 residues processed: 571 average time/residue: 1.6239 time to fit residues: 1045.8301 Evaluate side-chains 546 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 505 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 203 SER 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 708 ASP Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1079 ASP 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 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 583 LEU 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 C residue 92 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 473 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS B 766 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24382 Z= 0.221 Angle : 0.692 11.569 32973 Z= 0.347 Chirality : 0.040 0.277 3738 Planarity : 0.004 0.051 4188 Dihedral : 6.320 151.234 3273 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.18 % Allowed : 23.72 % Favored : 74.10 % 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: 2.39 (0.16), residues: 2920 helix: 2.45 (0.12), residues: 1927 sheet: 1.23 (0.47), residues: 109 loop : -0.33 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 86 HIS 0.007 0.001 HIS A1058 PHE 0.020 0.001 PHE G 28 TYR 0.026 0.001 TYR B 930 ARG 0.013 0.001 ARG A 388 *********************** 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 579 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 521 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7881 (mmm) cc_final: 0.7352 (mmm) REVERT: A 114 VAL cc_start: 0.8757 (t) cc_final: 0.8475 (p) REVERT: A 148 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6544 (ttm-80) REVERT: A 310 ASP cc_start: 0.7521 (t0) cc_final: 0.7294 (t0) REVERT: A 650 ASP cc_start: 0.7229 (t70) cc_final: 0.7022 (t0) REVERT: A 964 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6931 (mtt-85) REVERT: B 405 ILE cc_start: 0.8200 (pp) cc_final: 0.7907 (mm) REVERT: B 510 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.5888 (mtp85) REVERT: B 725 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7629 (mtm) REVERT: G 63 ASP cc_start: 0.7103 (p0) cc_final: 0.6773 (p0) outliers start: 58 outliers final: 31 residues processed: 549 average time/residue: 1.5790 time to fit residues: 976.1491 Evaluate side-chains 536 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 502 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 203 SER 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 763 ASP 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 177 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 583 LEU 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 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 VAL 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: 3.9990 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 139 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 218 ASN A 328 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A1029 GLN A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4068 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= 0.209 Angle : 0.711 12.224 32973 Z= 0.353 Chirality : 0.040 0.258 3738 Planarity : 0.004 0.060 4188 Dihedral : 6.321 150.881 3273 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.84 % Allowed : 24.59 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2920 helix: 2.47 (0.12), residues: 1934 sheet: 1.21 (0.47), residues: 109 loop : -0.37 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 97 HIS 0.008 0.001 HIS A1058 PHE 0.026 0.001 PHE B 521 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 573 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 524 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7825 (mmm) cc_final: 0.7326 (mmm) REVERT: A 148 ARG cc_start: 0.6779 (tpp80) cc_final: 0.6529 (ttm-80) REVERT: A 310 ASP cc_start: 0.7488 (t0) cc_final: 0.7254 (t0) REVERT: A 344 ASN cc_start: 0.7226 (p0) cc_final: 0.6829 (p0) REVERT: A 650 ASP cc_start: 0.7216 (t70) cc_final: 0.6928 (t0) REVERT: A 1051 GLU cc_start: 0.7285 (pp20) cc_final: 0.7067 (pp20) REVERT: B 510 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.5785 (mtp85) REVERT: F 156 GLU cc_start: 0.7289 (mp0) cc_final: 0.6660 (mp0) REVERT: G 63 ASP cc_start: 0.7108 (p0) cc_final: 0.6760 (p0) REVERT: G 170 ASP cc_start: 0.7577 (t70) cc_final: 0.7323 (t0) outliers start: 49 outliers final: 30 residues processed: 548 average time/residue: 1.5495 time to fit residues: 959.9039 Evaluate side-chains 537 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 506 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 203 SER 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 1068 THR Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 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 68 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 218 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN C 70 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24382 Z= 0.228 Angle : 0.747 12.859 32973 Z= 0.371 Chirality : 0.040 0.244 3738 Planarity : 0.004 0.056 4188 Dihedral : 6.217 150.832 3269 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.76 % Allowed : 25.53 % 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: 2.37 (0.16), residues: 2920 helix: 2.43 (0.12), residues: 1946 sheet: 1.02 (0.46), residues: 119 loop : -0.40 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 97 HIS 0.008 0.001 HIS A1058 PHE 0.031 0.001 PHE G 28 TYR 0.029 0.001 TYR B 565 ARG 0.013 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 566 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 519 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7821 (mmm) cc_final: 0.7326 (mmm) REVERT: A 148 ARG cc_start: 0.6812 (tpp80) cc_final: 0.6566 (ttm-80) REVERT: A 212 MET cc_start: 0.7525 (mmt) cc_final: 0.7318 (mmt) REVERT: A 310 ASP cc_start: 0.7452 (t0) cc_final: 0.7154 (t0) REVERT: A 344 ASN cc_start: 0.7197 (p0) cc_final: 0.6789 (p0) REVERT: B 78 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7216 (tm-30) REVERT: B 402 ASP cc_start: 0.7038 (t0) cc_final: 0.6824 (t0) REVERT: B 405 ILE cc_start: 0.8187 (pp) cc_final: 0.7815 (mm) REVERT: B 510 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.5782 (mtp85) REVERT: B 731 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: G 63 ASP cc_start: 0.7110 (p0) cc_final: 0.6760 (p0) REVERT: G 126 ILE cc_start: 0.8045 (pp) cc_final: 0.7798 (pt) REVERT: G 170 ASP cc_start: 0.7579 (t70) cc_final: 0.7326 (t0) outliers start: 47 outliers final: 33 residues processed: 542 average time/residue: 1.5572 time to fit residues: 951.6296 Evaluate side-chains 539 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 504 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 GLN 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 891 SER Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 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 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 45 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 267 optimal weight: 0.4980 chunk 231 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24382 Z= 0.239 Angle : 0.767 12.466 32973 Z= 0.380 Chirality : 0.041 0.225 3738 Planarity : 0.005 0.069 4188 Dihedral : 6.224 150.900 3269 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.69 % Allowed : 25.71 % Favored : 72.60 % 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: 2.34 (0.16), residues: 2920 helix: 2.40 (0.12), residues: 1945 sheet: 0.98 (0.46), residues: 119 loop : -0.40 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 97 HIS 0.008 0.001 HIS A1058 PHE 0.022 0.001 PHE B 521 TYR 0.031 0.001 TYR F 154 ARG 0.015 0.001 ARG B 547 ********************** 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 560 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 515 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7825 (mmm) cc_final: 0.7321 (mmm) REVERT: A 148 ARG cc_start: 0.6881 (tpp80) cc_final: 0.6655 (ttm-80) REVERT: A 310 ASP cc_start: 0.7375 (t0) cc_final: 0.7162 (t0) REVERT: A 344 ASN cc_start: 0.7191 (p0) cc_final: 0.6784 (p0) REVERT: B 78 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7262 (tm-30) REVERT: B 405 ILE cc_start: 0.8203 (pp) cc_final: 0.7857 (mm) REVERT: B 510 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.5794 (mtp85) REVERT: B 731 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: G 63 ASP cc_start: 0.7115 (p0) cc_final: 0.6764 (p0) REVERT: G 170 ASP cc_start: 0.7591 (t70) cc_final: 0.7337 (t0) outliers start: 45 outliers final: 36 residues processed: 536 average time/residue: 1.5955 time to fit residues: 966.8499 Evaluate side-chains 545 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 507 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 GLN 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 891 SER Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 549 PHE 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 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 47 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 213 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- 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 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 766 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.089930 restraints weight = 49541.943| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.71 r_work: 0.3338 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24382 Z= 0.254 Angle : 0.783 12.945 32973 Z= 0.388 Chirality : 0.041 0.232 3738 Planarity : 0.005 0.059 4188 Dihedral : 6.223 151.192 3269 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.58 % Allowed : 26.05 % Favored : 72.37 % 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: 2.30 (0.16), residues: 2920 helix: 2.40 (0.12), residues: 1935 sheet: 0.96 (0.46), residues: 119 loop : -0.42 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 97 HIS 0.011 0.001 HIS A1058 PHE 0.029 0.001 PHE G 28 TYR 0.032 0.001 TYR F 154 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: 13336.18 seconds wall clock time: 233 minutes 20.99 seconds (14000.99 seconds total)