Starting phenix.real_space_refine on Mon Nov 18 01:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/11_2024/8pbx_17587.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/11_2024/8pbx_17587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/11_2024/8pbx_17587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/11_2024/8pbx_17587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/11_2024/8pbx_17587.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/11_2024/8pbx_17587.cif" } resolution = 3.3 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= 0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16861 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 10715 2.51 5 N 2864 2.21 5 O 3394 1.98 5 H 16455 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 33448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 13661 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 40, 'TRANS': 861} Chain breaks: 2 Chain: "B" Number of atoms: 19787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 19787 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 80, 'TRANS': 1204} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 14.11, per 1000 atoms: 0.42 Number of scatterers: 33448 At special positions: 0 Unit cell: (91.35, 128.1, 135.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 3394 8.00 N 2864 7.00 C 10715 6.00 H 16455 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.30 Conformation dependent library (CDL) restraints added in 2.5 seconds 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 37 sheets defined 23.0% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 138 through 148 removed outlier: 3.923A pdb=" N GLN A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.664A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 490 through 495 removed outlier: 4.455A pdb=" N SER A 494 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 548 through 561 removed outlier: 4.219A pdb=" N SER A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.532A pdb=" N THR A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.578A pdb=" N THR A 754 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 3.588A pdb=" N SER A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 858 through 864 Processing helix chain 'A' and resid 865 through 870 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.874A pdb=" N GLY B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 125 " --> pdb=" O TYR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.830A pdb=" N GLU B 254 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 334 through 337 removed outlier: 3.589A pdb=" N GLY B 337 " --> pdb=" O LYS B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 369 through 370 No H-bonds generated for 'chain 'B' and resid 369 through 370' Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.726A pdb=" N TRP B 408 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 409 " --> pdb=" O PRO B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 409' Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.565A pdb=" N ILE B 628 " --> pdb=" O ASN B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 641 Processing helix chain 'B' and resid 661 through 670 Processing helix chain 'B' and resid 699 through 706 Processing helix chain 'B' and resid 721 through 727 removed outlier: 4.292A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 745 removed outlier: 4.180A pdb=" N ASN B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.962A pdb=" N ASP B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 838 through 842 removed outlier: 3.585A pdb=" N LYS B 842 " --> pdb=" O ALA B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 917 removed outlier: 3.510A pdb=" N GLN B 909 " --> pdb=" O PRO B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 944 removed outlier: 3.726A pdb=" N THR B 944 " --> pdb=" O TRP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 950 Processing helix chain 'B' and resid 961 through 970 Processing helix chain 'B' and resid 1051 through 1056 Processing helix chain 'B' and resid 1059 through 1062 Processing helix chain 'B' and resid 1130 through 1136 removed outlier: 4.304A pdb=" N ALA B1134 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR B1135 " --> pdb=" O SER B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1142 Processing helix chain 'B' and resid 1145 through 1154 removed outlier: 3.583A pdb=" N ILE B1149 " --> pdb=" O THR B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1161 Processing helix chain 'B' and resid 1192 through 1203 Processing helix chain 'B' and resid 1204 through 1211 removed outlier: 4.224A pdb=" N LYS B1208 " --> pdb=" O GLN B1205 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER B1209 " --> pdb=" O ASN B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1245 through 1249 Processing helix chain 'B' and resid 1255 through 1259 Processing helix chain 'B' and resid 1260 through 1266 Processing helix chain 'B' and resid 1268 through 1273 removed outlier: 3.906A pdb=" N PHE B1273 " --> pdb=" O VAL B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1287 Proline residue: B1286 - end of helix Processing helix chain 'B' and resid 1296 through 1298 No H-bonds generated for 'chain 'B' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 71 removed outlier: 6.516A pdb=" N LEU A 79 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A 69 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 77 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 128 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR A 115 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N MET A 126 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 215 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 304 removed outlier: 3.513A pdb=" N MET A 312 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 391 removed outlier: 5.028A pdb=" N ILE A 385 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 400 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE A 541 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 425 removed outlier: 3.949A pdb=" N GLY A 406 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 458 through 459 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.792A pdb=" N GLY A 477 " --> pdb=" O THR A 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 626 through 633 removed outlier: 5.536A pdb=" N GLY A 628 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 651 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 649 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 704 removed outlier: 5.582A pdb=" N PHE A 698 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP A 715 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 700 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 709 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 740 " --> pdb=" O TRP A 710 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE A 769 " --> pdb=" O VAL A 737 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 739 " --> pdb=" O SER A 767 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER A 767 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER A 741 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL A 765 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 775 through 780 removed outlier: 5.094A pdb=" N LEU A 776 " --> pdb=" O LYS A 792 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS A 792 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 800 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 808 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 840 through 843 Processing sheet with id=AB8, first strand: chain 'A' and resid 884 through 892 removed outlier: 6.157A pdb=" N SER A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 884 through 892 removed outlier: 6.157A pdb=" N SER A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 915 through 916 removed outlier: 3.623A pdb=" N VAL A 919 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.762A pdb=" N ARG B 132 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AC4, first strand: chain 'B' and resid 187 through 193 removed outlier: 6.553A pdb=" N LEU B 204 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 191 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN B 193 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU B 200 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 340 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 358 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER B 342 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AC6, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.551A pdb=" N LYS B 876 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 277 through 279 removed outlier: 3.596A pdb=" N LEU B 277 " --> pdb=" O VAL B 653 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 281 through 282 removed outlier: 3.797A pdb=" N LYS B 292 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 457 through 460 removed outlier: 3.554A pdb=" N LYS B 497 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 545 removed outlier: 5.160A pdb=" N VAL B 539 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 554 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 549 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 695 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 750 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 697 " --> pdb=" O GLN B 748 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD3, first strand: chain 'B' and resid 845 through 846 Processing sheet with id=AD4, first strand: chain 'B' and resid 921 through 923 Processing sheet with id=AD5, first strand: chain 'B' and resid 1009 through 1014 removed outlier: 5.288A pdb=" N GLN B1023 " --> pdb=" O GLY B1010 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B1012 " --> pdb=" O GLY B1021 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B1021 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B1020 " --> pdb=" O PHE B1031 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 4.900A pdb=" N GLY B1066 " --> pdb=" O LEU B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1228 through 1230 Processing sheet with id=AD8, first strand: chain 'B' and resid 1252 through 1253 removed outlier: 3.600A pdb=" N SER B1252 " --> pdb=" O ASN B1290 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1300 through 1307 removed outlier: 6.920A pdb=" N ILE B1300 " --> pdb=" O LYS B1321 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B1321 " --> pdb=" O ILE B1300 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B1302 " --> pdb=" O GLU B1319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU B1319 " --> pdb=" O LEU B1302 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B1304 " --> pdb=" O ARG B1317 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG B1317 " --> pdb=" O VAL B1304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1300 through 1307 removed outlier: 6.920A pdb=" N ILE B1300 " --> pdb=" O LYS B1321 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B1321 " --> pdb=" O ILE B1300 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B1302 " --> pdb=" O GLU B1319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU B1319 " --> pdb=" O LEU B1302 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B1304 " --> pdb=" O ARG B1317 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG B1317 " --> pdb=" O VAL B1304 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1131 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: 13.53 Time building geometry restraints manager: 9.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16455 1.03 - 1.23: 6 1.23 - 1.42: 7395 1.42 - 1.61: 9950 1.61 - 1.81: 40 Bond restraints: 33846 Sorted by residual: bond pdb=" C VAL B 653 " pdb=" N TYR B 654 " ideal model delta sigma weight residual 1.329 1.290 0.038 1.60e-02 3.91e+03 5.77e+00 bond pdb=" N GLN B 59 " pdb=" CA GLN B 59 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N THR A 27 " pdb=" CA THR A 27 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" N THR A 27 " pdb=" H THR A 27 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" N GLN B 59 " pdb=" H GLN B 59 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 33841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 60150 1.65 - 3.29: 782 3.29 - 4.94: 98 4.94 - 6.58: 0 6.58 - 8.23: 1 Bond angle restraints: 61031 Sorted by residual: angle pdb=" N VAL A 604 " pdb=" CA VAL A 604 " pdb=" C VAL A 604 " ideal model delta sigma weight residual 113.53 109.82 3.71 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N GLY B 383 " pdb=" CA GLY B 383 " pdb=" C GLY B 383 " ideal model delta sigma weight residual 111.35 115.46 -4.11 1.20e+00 6.94e-01 1.18e+01 angle pdb=" N ILE A 868 " pdb=" CA ILE A 868 " pdb=" C ILE A 868 " ideal model delta sigma weight residual 112.35 108.35 4.00 1.41e+00 5.03e-01 8.04e+00 angle pdb=" CB MET A 141 " pdb=" CG MET A 141 " pdb=" SD MET A 141 " ideal model delta sigma weight residual 112.70 120.93 -8.23 3.00e+00 1.11e-01 7.52e+00 angle pdb=" N VAL B 189 " pdb=" CA VAL B 189 " pdb=" C VAL B 189 " ideal model delta sigma weight residual 113.71 111.13 2.58 9.50e-01 1.11e+00 7.40e+00 ... (remaining 61026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14346 17.99 - 35.98: 1294 35.98 - 53.97: 405 53.97 - 71.96: 112 71.96 - 89.95: 36 Dihedral angle restraints: 16193 sinusoidal: 8727 harmonic: 7466 Sorted by residual: dihedral pdb=" CA SER A 367 " pdb=" C SER A 367 " pdb=" N THR A 368 " pdb=" CA THR A 368 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASN B 668 " pdb=" C ASN B 668 " pdb=" N TRP B 669 " pdb=" CA TRP B 669 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 451 " pdb=" C PHE B 451 " pdb=" N ALA B 452 " pdb=" CA ALA B 452 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 16190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2236 0.056 - 0.111: 333 0.111 - 0.167: 57 0.167 - 0.223: 0 0.223 - 0.279: 1 Chirality restraints: 2627 Sorted by residual: chirality pdb=" CB VAL A 443 " pdb=" CA VAL A 443 " pdb=" CG1 VAL A 443 " pdb=" CG2 VAL A 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 603 " pdb=" N ILE B 603 " pdb=" C ILE B 603 " pdb=" CB ILE B 603 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2624 not shown) Planarity restraints: 5172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 669 " 0.027 2.00e-02 2.50e+03 1.76e-02 1.24e+01 pdb=" CG TRP B 669 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 669 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 669 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 669 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 669 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 669 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 669 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 669 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 669 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP B 669 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP B 669 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP B 669 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 669 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 669 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 669 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 625 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 626 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 600 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 601 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 601 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 601 " -0.025 5.00e-02 4.00e+02 ... (remaining 5169 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1349 2.12 - 2.74: 63188 2.74 - 3.36: 99958 3.36 - 3.98: 131274 3.98 - 4.60: 203908 Nonbonded interactions: 499677 Sorted by model distance: nonbonded pdb=" OE1 GLN A 380 " pdb=" H ALA A 382 " model vdw 1.505 2.450 nonbonded pdb=" OE1 GLU B 83 " pdb=" H GLU B 83 " model vdw 1.529 2.450 nonbonded pdb=" HE1 TRP B 374 " pdb=" O PHE B 531 " model vdw 1.541 2.450 nonbonded pdb="HE21 GLN B 906 " pdb=" O ASN B 958 " model vdw 1.545 2.450 nonbonded pdb=" O GLY B 917 " pdb=" HG SER B1000 " model vdw 1.545 2.450 ... (remaining 499672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.530 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 65.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 0.038 17391 Z= 0.307 Angle : 0.591 8.227 23670 Z= 0.323 Chirality : 0.043 0.279 2627 Planarity : 0.004 0.052 3110 Dihedral : 15.134 89.593 6286 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 0.26 % Allowed : 16.03 % Favored : 83.71 % 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: -0.66 (0.18), residues: 2177 helix: -0.35 (0.28), residues: 353 sheet: 0.06 (0.28), residues: 330 loop : -0.56 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 669 HIS 0.006 0.001 HIS B 352 PHE 0.022 0.002 PHE B 451 TYR 0.014 0.002 TYR A 296 ARG 0.006 0.001 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 239 time to evaluate : 2.349 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 GLU cc_start: 0.6409 (tt0) cc_final: 0.6194 (tt0) outliers start: 5 outliers final: 4 residues processed: 241 average time/residue: 0.5733 time to fit residues: 220.7267 Evaluate side-chains 238 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 234 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 760 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 170 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17391 Z= 0.204 Angle : 0.551 4.964 23670 Z= 0.292 Chirality : 0.043 0.198 2627 Planarity : 0.004 0.047 3110 Dihedral : 5.112 43.059 2311 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.49 % Rotamer: Outliers : 1.10 % Allowed : 14.46 % Favored : 84.44 % 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: -0.56 (0.18), residues: 2177 helix: -0.26 (0.29), residues: 348 sheet: 0.03 (0.28), residues: 336 loop : -0.46 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 669 HIS 0.007 0.001 HIS B 352 PHE 0.016 0.001 PHE B 451 TYR 0.010 0.001 TYR A 383 ARG 0.003 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 258 average time/residue: 0.5464 time to fit residues: 228.4943 Evaluate side-chains 250 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 141 TYR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1003 ASN Chi-restraints excluded: chain B residue 1243 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 214 optimal weight: 0.0770 chunk 176 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 684 ASN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17391 Z= 0.237 Angle : 0.533 4.970 23670 Z= 0.279 Chirality : 0.042 0.183 2627 Planarity : 0.004 0.052 3110 Dihedral : 5.035 44.624 2308 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 0.94 % Allowed : 15.45 % Favored : 83.60 % 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: -0.71 (0.18), residues: 2177 helix: -0.26 (0.28), residues: 355 sheet: -0.27 (0.27), residues: 348 loop : -0.55 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.016 0.001 PHE B 451 TYR 0.010 0.001 TYR A 296 ARG 0.004 0.000 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 2.594 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: B 119 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: B 662 TYR cc_start: 0.7310 (t80) cc_final: 0.6976 (t80) outliers start: 18 outliers final: 13 residues processed: 246 average time/residue: 0.5622 time to fit residues: 224.4896 Evaluate side-chains 241 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 227 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17391 Z= 0.370 Angle : 0.571 4.983 23670 Z= 0.302 Chirality : 0.043 0.190 2627 Planarity : 0.004 0.058 3110 Dihedral : 5.109 39.860 2305 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.80 % Favored : 93.06 % Rotamer: Outliers : 1.36 % Allowed : 15.30 % Favored : 83.34 % 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: -0.96 (0.18), residues: 2177 helix: -0.47 (0.28), residues: 355 sheet: -0.46 (0.27), residues: 348 loop : -0.72 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 669 HIS 0.006 0.001 HIS B 352 PHE 0.023 0.002 PHE B 451 TYR 0.017 0.002 TYR A 296 ARG 0.005 0.001 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 2.703 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LYS cc_start: 0.8652 (tptt) cc_final: 0.8389 (tptt) REVERT: A 582 TYR cc_start: 0.8272 (p90) cc_final: 0.7864 (p90) REVERT: A 903 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7454 (tp-100) REVERT: B 1328 PHE cc_start: 0.8510 (m-80) cc_final: 0.8170 (m-80) outliers start: 26 outliers final: 23 residues processed: 248 average time/residue: 0.5575 time to fit residues: 223.6777 Evaluate side-chains 251 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 646 ASN Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17391 Z= 0.287 Angle : 0.545 4.859 23670 Z= 0.286 Chirality : 0.043 0.182 2627 Planarity : 0.004 0.059 3110 Dihedral : 5.060 38.129 2305 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.29 % Favored : 93.57 % Rotamer: Outliers : 1.68 % Allowed : 15.87 % Favored : 82.45 % 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: -0.98 (0.18), residues: 2177 helix: -0.45 (0.28), residues: 355 sheet: -0.54 (0.27), residues: 348 loop : -0.72 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.020 0.001 PHE B 451 TYR 0.013 0.001 TYR A 296 ARG 0.004 0.000 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 2.496 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LYS cc_start: 0.8647 (tptt) cc_final: 0.8411 (tptt) REVERT: A 582 TYR cc_start: 0.8224 (p90) cc_final: 0.7770 (p90) REVERT: A 903 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7462 (tp-100) REVERT: B 201 TYR cc_start: 0.6889 (m-80) cc_final: 0.6544 (m-80) REVERT: B 1328 PHE cc_start: 0.8521 (m-80) cc_final: 0.8205 (m-80) outliers start: 32 outliers final: 23 residues processed: 250 average time/residue: 0.5690 time to fit residues: 227.0023 Evaluate side-chains 248 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1003 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17391 Z= 0.311 Angle : 0.547 5.656 23670 Z= 0.287 Chirality : 0.043 0.197 2627 Planarity : 0.004 0.059 3110 Dihedral : 5.049 34.915 2305 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.03 % Favored : 92.83 % Rotamer: Outliers : 1.41 % Allowed : 16.40 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2177 helix: -0.44 (0.28), residues: 355 sheet: -0.64 (0.27), residues: 348 loop : -0.78 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.021 0.001 PHE B 451 TYR 0.014 0.001 TYR A 296 ARG 0.003 0.000 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 2.492 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LYS cc_start: 0.8645 (tptt) cc_final: 0.8432 (tptt) REVERT: A 582 TYR cc_start: 0.8271 (p90) cc_final: 0.7745 (p90) REVERT: A 903 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7502 (tp-100) REVERT: B 201 TYR cc_start: 0.6834 (m-80) cc_final: 0.6464 (m-80) REVERT: B 1328 PHE cc_start: 0.8505 (m-80) cc_final: 0.8269 (m-80) outliers start: 27 outliers final: 23 residues processed: 251 average time/residue: 0.5699 time to fit residues: 228.6294 Evaluate side-chains 250 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1003 ASN Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17391 Z= 0.381 Angle : 0.577 5.297 23670 Z= 0.304 Chirality : 0.043 0.184 2627 Planarity : 0.004 0.058 3110 Dihedral : 5.176 29.830 2305 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.67 % Favored : 92.19 % Rotamer: Outliers : 1.89 % Allowed : 16.13 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2177 helix: -0.62 (0.27), residues: 362 sheet: -0.84 (0.27), residues: 353 loop : -0.94 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.024 0.002 PHE B 451 TYR 0.018 0.002 TYR A 296 ARG 0.003 0.000 ARG B 907 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 2.549 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 TYR cc_start: 0.8330 (p90) cc_final: 0.7740 (p90) REVERT: A 826 LEU cc_start: 0.8493 (tp) cc_final: 0.8268 (tp) REVERT: A 903 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7591 (tp-100) REVERT: B 201 TYR cc_start: 0.6931 (m-80) cc_final: 0.6471 (m-80) REVERT: B 407 GLU cc_start: 0.7691 (mp0) cc_final: 0.7259 (mp0) REVERT: B 1328 PHE cc_start: 0.8517 (m-80) cc_final: 0.8301 (m-80) outliers start: 36 outliers final: 30 residues processed: 250 average time/residue: 0.5704 time to fit residues: 230.7670 Evaluate side-chains 246 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17391 Z= 0.252 Angle : 0.540 4.660 23670 Z= 0.282 Chirality : 0.042 0.192 2627 Planarity : 0.004 0.056 3110 Dihedral : 5.041 29.864 2305 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 1.47 % Allowed : 16.61 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2177 helix: -0.41 (0.28), residues: 355 sheet: -0.79 (0.27), residues: 348 loop : -0.81 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 669 HIS 0.012 0.001 HIS B 352 PHE 0.019 0.001 PHE B 451 TYR 0.012 0.001 TYR A 157 ARG 0.003 0.000 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 2.565 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 TYR cc_start: 0.8324 (p90) cc_final: 0.7753 (p90) REVERT: A 826 LEU cc_start: 0.8492 (tp) cc_final: 0.8255 (tp) REVERT: A 903 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7580 (tp-100) REVERT: B 201 TYR cc_start: 0.6895 (m-80) cc_final: 0.6519 (m-80) REVERT: B 557 MET cc_start: 0.8709 (mtt) cc_final: 0.8186 (mtt) REVERT: B 1328 PHE cc_start: 0.8496 (m-80) cc_final: 0.8270 (m-80) outliers start: 28 outliers final: 25 residues processed: 243 average time/residue: 0.5603 time to fit residues: 220.5711 Evaluate side-chains 248 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 0.0170 chunk 201 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 60 optimal weight: 0.0370 chunk 176 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17391 Z= 0.236 Angle : 0.535 7.023 23670 Z= 0.280 Chirality : 0.042 0.192 2627 Planarity : 0.004 0.055 3110 Dihedral : 4.957 29.496 2305 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 1.26 % Allowed : 16.92 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2177 helix: -0.33 (0.28), residues: 355 sheet: -0.78 (0.27), residues: 348 loop : -0.76 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 669 HIS 0.011 0.001 HIS B 352 PHE 0.019 0.001 PHE B 451 TYR 0.012 0.001 TYR B1307 ARG 0.002 0.000 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 2.514 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 TYR cc_start: 0.8319 (p90) cc_final: 0.7764 (p90) REVERT: A 826 LEU cc_start: 0.8472 (tp) cc_final: 0.8239 (tp) REVERT: A 903 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7588 (tp-100) REVERT: B 179 ASP cc_start: 0.8108 (m-30) cc_final: 0.7811 (t0) REVERT: B 201 TYR cc_start: 0.6869 (m-80) cc_final: 0.6411 (m-80) REVERT: B 557 MET cc_start: 0.8686 (mtt) cc_final: 0.8141 (mtt) outliers start: 24 outliers final: 22 residues processed: 240 average time/residue: 0.5590 time to fit residues: 216.6564 Evaluate side-chains 240 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 2.9990 chunk 126 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17391 Z= 0.212 Angle : 0.526 4.867 23670 Z= 0.274 Chirality : 0.042 0.210 2627 Planarity : 0.004 0.054 3110 Dihedral : 4.894 29.440 2305 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 1.15 % Allowed : 16.97 % Favored : 81.88 % 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: -0.99 (0.18), residues: 2177 helix: -0.23 (0.29), residues: 355 sheet: -0.82 (0.27), residues: 353 loop : -0.71 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 669 HIS 0.011 0.001 HIS B 352 PHE 0.047 0.001 PHE B1328 TYR 0.013 0.001 TYR B1307 ARG 0.002 0.000 ARG B1301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 2.516 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 TYR cc_start: 0.8308 (p90) cc_final: 0.7762 (p90) REVERT: A 826 LEU cc_start: 0.8446 (tp) cc_final: 0.8211 (tp) REVERT: A 903 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7624 (tp-100) REVERT: B 201 TYR cc_start: 0.6832 (m-80) cc_final: 0.6381 (m-80) REVERT: B 557 MET cc_start: 0.8702 (mtt) cc_final: 0.8294 (mtt) REVERT: B 669 TRP cc_start: 0.8790 (m-10) cc_final: 0.8463 (m-10) REVERT: B 1210 GLU cc_start: 0.8010 (tt0) cc_final: 0.7798 (tt0) outliers start: 22 outliers final: 21 residues processed: 241 average time/residue: 0.5715 time to fit residues: 222.5335 Evaluate side-chains 242 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 173 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.148913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121378 restraints weight = 72084.218| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.27 r_work: 0.3523 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17391 Z= 0.291 Angle : 0.545 4.963 23670 Z= 0.285 Chirality : 0.042 0.200 2627 Planarity : 0.004 0.056 3110 Dihedral : 4.951 28.289 2305 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 1.31 % Allowed : 17.08 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2177 helix: -0.30 (0.28), residues: 356 sheet: -0.94 (0.27), residues: 360 loop : -0.77 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 669 HIS 0.011 0.001 HIS B 352 PHE 0.030 0.002 PHE B1328 TYR 0.013 0.001 TYR A 296 ARG 0.006 0.000 ARG B1301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6609.01 seconds wall clock time: 117 minutes 0.14 seconds (7020.14 seconds total)