Starting phenix.real_space_refine on Tue Sep 24 17:03:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/09_2024/5mz6_3583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/09_2024/5mz6_3583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/09_2024/5mz6_3583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/09_2024/5mz6_3583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/09_2024/5mz6_3583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/09_2024/5mz6_3583.cif" } resolution = 3.8 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= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5339 2.51 5 N 1457 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8401 Number of models: 1 Model: "" Number of chains: 2 Chain: "1" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7968 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 32, 'TRANS': 985} Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 433 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 5.24, per 1000 atoms: 0.62 Number of scatterers: 8401 At special positions: 0 Unit cell: (88.66, 124.41, 74.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1535 8.00 N 1457 7.00 C 5339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 11031 " - pdb=" SG CYS 11066 " distance=2.02 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: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 63.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain '1' and resid 12 through 41 removed outlier: 3.938A pdb=" N LEU 1 16 " --> pdb=" O HIS 1 12 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU 1 18 " --> pdb=" O GLU 1 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS 1 21 " --> pdb=" O ASP 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 49 removed outlier: 4.045A pdb=" N ILE 1 46 " --> pdb=" O SER 1 42 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 58 No H-bonds generated for 'chain '1' and resid 56 through 58' Processing helix chain '1' and resid 59 through 72 removed outlier: 3.940A pdb=" N ARG 1 65 " --> pdb=" O SER 1 61 " (cutoff:3.500A) Processing helix chain '1' and resid 78 through 96 removed outlier: 4.198A pdb=" N TYR 1 82 " --> pdb=" O GLY 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 102 Processing helix chain '1' and resid 103 through 104 No H-bonds generated for 'chain '1' and resid 103 through 104' Processing helix chain '1' and resid 105 through 109 removed outlier: 3.531A pdb=" N ARG 1 108 " --> pdb=" O SER 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 125 removed outlier: 3.955A pdb=" N LEU 1 118 " --> pdb=" O ILE 1 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE 1 123 " --> pdb=" O CYS 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 127 through 143 removed outlier: 4.068A pdb=" N VAL 1 133 " --> pdb=" O CYS 1 129 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS 1 134 " --> pdb=" O ARG 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 144 through 149 Processing helix chain '1' and resid 150 through 158 removed outlier: 3.820A pdb=" N LEU 1 155 " --> pdb=" O ALA 1 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET 1 156 " --> pdb=" O LEU 1 152 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 171 removed outlier: 3.751A pdb=" N ILE 1 164 " --> pdb=" O GLU 1 160 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU 1 165 " --> pdb=" O THR 1 161 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS 1 166 " --> pdb=" O GLU 1 162 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 1 170 " --> pdb=" O LYS 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 193 removed outlier: 3.630A pdb=" N ALA 1 183 " --> pdb=" O ASP 1 179 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 1 184 " --> pdb=" O MET 1 180 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU 1 191 " --> pdb=" O ALA 1 187 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS 1 192 " --> pdb=" O MET 1 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS 1 193 " --> pdb=" O ASN 1 189 " (cutoff:3.500A) Processing helix chain '1' and resid 198 through 214 removed outlier: 3.848A pdb=" N GLU 1 202 " --> pdb=" O VAL 1 198 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP 1 209 " --> pdb=" O MET 1 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS 1 212 " --> pdb=" O ARG 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 218 through 232 removed outlier: 3.701A pdb=" N TYR 1 227 " --> pdb=" O GLU 1 223 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 1 229 " --> pdb=" O ALA 1 225 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 237 removed outlier: 4.267A pdb=" N SER 1 236 " --> pdb=" O SER 1 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN 1 237 " --> pdb=" O THR 1 234 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 233 through 237' Processing helix chain '1' and resid 251 through 257 removed outlier: 4.165A pdb=" N HIS 1 255 " --> pdb=" O ASP 1 251 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN 1 257 " --> pdb=" O VAL 1 253 " (cutoff:3.500A) Processing helix chain '1' and resid 258 through 271 removed outlier: 3.613A pdb=" N SER 1 263 " --> pdb=" O ALA 1 259 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP 1 264 " --> pdb=" O ALA 1 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 1 267 " --> pdb=" O SER 1 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG 1 268 " --> pdb=" O ASP 1 264 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN 1 269 " --> pdb=" O SER 1 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG 1 270 " --> pdb=" O LEU 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 275 removed outlier: 4.123A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 272 through 275' Processing helix chain '1' and resid 304 through 321 removed outlier: 3.634A pdb=" N ILE 1 308 " --> pdb=" O ILE 1 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU 1 317 " --> pdb=" O GLU 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 329 through 346 removed outlier: 3.564A pdb=" N ALA 1 334 " --> pdb=" O ASP 1 330 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE 1 336 " --> pdb=" O MET 1 332 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN 1 338 " --> pdb=" O ALA 1 334 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL 1 341 " --> pdb=" O LEU 1 337 " (cutoff:3.500A) Processing helix chain '1' and resid 347 through 365 removed outlier: 3.632A pdb=" N THR 1 354 " --> pdb=" O ARG 1 350 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR 1 357 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER 1 362 " --> pdb=" O LEU 1 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER 1 363 " --> pdb=" O ALA 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 386 removed outlier: 4.175A pdb=" N VAL 1 379 " --> pdb=" O LYS 1 375 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER 1 380 " --> pdb=" O LEU 1 376 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL 1 382 " --> pdb=" O ARG 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 451 through 456 removed outlier: 3.897A pdb=" N ILE 1 455 " --> pdb=" O ASN 1 451 " (cutoff:3.500A) Processing helix chain '1' and resid 459 through 475 removed outlier: 3.563A pdb=" N ALA 1 464 " --> pdb=" O SER 1 460 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET 1 467 " --> pdb=" O ALA 1 463 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 495 removed outlier: 3.545A pdb=" N ASP 1 486 " --> pdb=" O LYS 1 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU 1 487 " --> pdb=" O HIS 1 483 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 1 489 " --> pdb=" O ASN 1 485 " (cutoff:3.500A) Processing helix chain '1' and resid 495 through 504 removed outlier: 3.829A pdb=" N GLN 1 499 " --> pdb=" O GLY 1 495 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 1 502 " --> pdb=" O SER 1 498 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS 1 503 " --> pdb=" O GLN 1 499 " (cutoff:3.500A) Processing helix chain '1' and resid 513 through 535 removed outlier: 3.519A pdb=" N LYS 1 530 " --> pdb=" O ARG 1 526 " (cutoff:3.500A) Processing helix chain '1' and resid 539 through 554 removed outlier: 3.960A pdb=" N MET 1 543 " --> pdb=" O ASP 1 539 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS 1 551 " --> pdb=" O ASN 1 547 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL 1 553 " --> pdb=" O ALA 1 549 " (cutoff:3.500A) Processing helix chain '1' and resid 560 through 576 removed outlier: 3.826A pdb=" N ALA 1 566 " --> pdb=" O ASP 1 562 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL 1 567 " --> pdb=" O MET 1 563 " (cutoff:3.500A) Processing helix chain '1' and resid 629 through 645 removed outlier: 3.987A pdb=" N VAL 1 635 " --> pdb=" O ARG 1 631 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG 1 636 " --> pdb=" O PHE 1 632 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA 1 638 " --> pdb=" O LYS 1 634 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN 1 641 " --> pdb=" O LEU 1 637 " (cutoff:3.500A) Processing helix chain '1' and resid 651 through 666 removed outlier: 3.589A pdb=" N ARG 1 657 " --> pdb=" O GLU 1 653 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA 1 660 " --> pdb=" O CYS 1 656 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR 1 661 " --> pdb=" O ARG 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 669 through 679 removed outlier: 3.604A pdb=" N TYR 1 674 " --> pdb=" O TRP 1 670 " (cutoff:3.500A) Processing helix chain '1' and resid 681 through 693 removed outlier: 3.903A pdb=" N ALA 1 687 " --> pdb=" O GLY 1 683 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 1 688 " --> pdb=" O ALA 1 684 " (cutoff:3.500A) Processing helix chain '1' and resid 703 through 715 removed outlier: 3.630A pdb=" N ARG 1 707 " --> pdb=" O SER 1 703 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR 1 710 " --> pdb=" O ASP 1 706 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS 1 711 " --> pdb=" O ARG 1 707 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 1 712 " --> pdb=" O PHE 1 708 " (cutoff:3.500A) Processing helix chain '1' and resid 751 through 774 removed outlier: 3.645A pdb=" N LYS 1 760 " --> pdb=" O GLU 1 756 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 1 767 " --> pdb=" O PHE 1 763 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP 1 768 " --> pdb=" O LEU 1 764 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 1 771 " --> pdb=" O GLU 1 767 " (cutoff:3.500A) Processing helix chain '1' and resid 779 through 805 removed outlier: 3.597A pdb=" N TRP 1 784 " --> pdb=" O PRO 1 780 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG 1 787 " --> pdb=" O PHE 1 783 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE 1 789 " --> pdb=" O LYS 1 785 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 1 790 " --> pdb=" O ARG 1 786 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP 1 799 " --> pdb=" O MET 1 795 " (cutoff:3.500A) Processing helix chain '1' and resid 806 through 814 removed outlier: 3.626A pdb=" N ALA 1 810 " --> pdb=" O GLY 1 807 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET 1 814 " --> pdb=" O SER 1 811 " (cutoff:3.500A) Processing helix chain '1' and resid 823 through 834 removed outlier: 3.628A pdb=" N ALA 1 827 " --> pdb=" O ALA 1 823 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 1 828 " --> pdb=" O ALA 1 824 " (cutoff:3.500A) Processing helix chain '1' and resid 839 through 847 removed outlier: 3.869A pdb=" N GLU 1 845 " --> pdb=" O GLY 1 841 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET 1 846 " --> pdb=" O GLU 1 842 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 1 847 " --> pdb=" O ALA 1 843 " (cutoff:3.500A) Processing helix chain '1' and resid 854 through 867 removed outlier: 3.605A pdb=" N LEU 1 863 " --> pdb=" O GLU 1 859 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS 1 866 " --> pdb=" O ILE 1 862 " (cutoff:3.500A) Processing helix chain '1' and resid 872 through 878 removed outlier: 3.572A pdb=" N LYS 1 876 " --> pdb=" O ASP 1 872 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER 1 877 " --> pdb=" O GLU 1 873 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE 1 878 " --> pdb=" O LYS 1 874 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 872 through 878' Processing helix chain '1' and resid 879 through 891 removed outlier: 4.012A pdb=" N HIS 1 883 " --> pdb=" O LEU 1 879 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU 1 888 " --> pdb=" O ARG 1 884 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN 1 891 " --> pdb=" O VAL 1 887 " (cutoff:3.500A) Processing helix chain '1' and resid 933 through 947 Processing helix chain '1' and resid 956 through 959 removed outlier: 3.873A pdb=" N ASN 1 959 " --> pdb=" O ASP 1 956 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 956 through 959' Processing helix chain '1' and resid 965 through 969 removed outlier: 3.755A pdb=" N ASN 1 968 " --> pdb=" O ASP 1 965 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN 1 969 " --> pdb=" O PRO 1 966 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 965 through 969' Processing helix chain '1' and resid 971 through 984 removed outlier: 3.636A pdb=" N LYS 1 975 " --> pdb=" O GLY 1 971 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL 1 978 " --> pdb=" O GLN 1 974 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 1 979 " --> pdb=" O LYS 1 975 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR 1 980 " --> pdb=" O ARG 1 976 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 1 983 " --> pdb=" O GLU 1 979 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE 1 984 " --> pdb=" O TYR 1 980 " (cutoff:3.500A) Processing helix chain '1' and resid 995 through 1006 Processing helix chain '1' and resid 1022 through 1027 removed outlier: 3.683A pdb=" N LEU 11026 " --> pdb=" O PRO 11022 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 11027 " --> pdb=" O ARG 11023 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1022 through 1027' Processing helix chain '1' and resid 1057 through 1064 removed outlier: 3.683A pdb=" N TYR 11061 " --> pdb=" O ALA 11057 " (cutoff:3.500A) Processing helix chain '1' and resid 1079 through 1094 removed outlier: 3.517A pdb=" N ASP 11090 " --> pdb=" O ILE 11086 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP 11091 " --> pdb=" O ARG 11087 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE 11093 " --> pdb=" O ILE 11089 " (cutoff:3.500A) Processing helix chain '1' and resid 1107 through 1119 removed outlier: 3.595A pdb=" N HIS 11113 " --> pdb=" O SER 11109 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER 11117 " --> pdb=" O HIS 11113 " (cutoff:3.500A) Processing helix chain '1' and resid 1125 through 1129 removed outlier: 3.753A pdb=" N VAL 11129 " --> pdb=" O GLY 11126 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 3.543A pdb=" N ALA B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 744 through 750 removed outlier: 7.004A pdb=" N ILE 1 732 " --> pdb=" O LEU 1 748 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN 1 931 " --> pdb=" O THR 1 903 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU 1 905 " --> pdb=" O GLN 1 931 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 953 through 955 removed outlier: 5.257A pdb=" N LEU 1 953 " --> pdb=" O VAL 11137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '1' and resid 987 through 990 removed outlier: 3.942A pdb=" N THR 1 989 " --> pdb=" O TYR 1 962 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU 1 964 " --> pdb=" O THR 1 989 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1137 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: 2.39 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2719 1.34 - 1.46: 1952 1.46 - 1.58: 3780 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 8566 Sorted by residual: bond pdb=" C ARG B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.30e+00 bond pdb=" C LEU 1 879 " pdb=" N PRO 1 880 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.11e-02 8.12e+03 3.20e+00 bond pdb=" C LEU 11134 " pdb=" N PRO 11135 " ideal model delta sigma weight residual 1.331 1.354 -0.023 1.31e-02 5.83e+03 3.17e+00 bond pdb=" CB ASP 1 137 " pdb=" CG ASP 1 137 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.03e+00 bond pdb=" C ILE 1 114 " pdb=" N PRO 1 115 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.70e+00 ... (remaining 8561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 11343 2.90 - 5.81: 208 5.81 - 8.71: 29 8.71 - 11.61: 4 11.61 - 14.52: 1 Bond angle restraints: 11585 Sorted by residual: angle pdb=" N PRO B 148 " pdb=" CA PRO B 148 " pdb=" CB PRO B 148 " ideal model delta sigma weight residual 103.36 110.53 -7.17 8.80e-01 1.29e+00 6.64e+01 angle pdb=" N PRO B 168 " pdb=" CA PRO B 168 " pdb=" CB PRO B 168 " ideal model delta sigma weight residual 103.08 110.27 -7.19 9.70e-01 1.06e+00 5.50e+01 angle pdb=" N PRO B 169 " pdb=" CA PRO B 169 " pdb=" CB PRO B 169 " ideal model delta sigma weight residual 103.25 109.99 -6.74 1.05e+00 9.07e-01 4.12e+01 angle pdb=" N PRO B 172 " pdb=" CA PRO B 172 " pdb=" CB PRO B 172 " ideal model delta sigma weight residual 103.44 110.10 -6.66 1.12e+00 7.97e-01 3.53e+01 angle pdb=" CA ALA 11064 " pdb=" C ALA 11064 " pdb=" O ALA 11064 " ideal model delta sigma weight residual 119.43 113.44 5.99 1.21e+00 6.83e-01 2.45e+01 ... (remaining 11580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 4813 15.03 - 30.07: 263 30.07 - 45.10: 94 45.10 - 60.13: 12 60.13 - 75.16: 6 Dihedral angle restraints: 5188 sinusoidal: 1973 harmonic: 3215 Sorted by residual: dihedral pdb=" CA ILE 1 951 " pdb=" C ILE 1 951 " pdb=" N PRO 1 952 " pdb=" CA PRO 1 952 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA HIS 1 255 " pdb=" C HIS 1 255 " pdb=" N ILE 1 256 " pdb=" CA ILE 1 256 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PRO B 141 " pdb=" C PRO B 141 " pdb=" N TYR B 142 " pdb=" CA TYR B 142 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1098 0.065 - 0.131: 185 0.131 - 0.196: 21 0.196 - 0.261: 4 0.261 - 0.327: 2 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CB VAL 1 928 " pdb=" CA VAL 1 928 " pdb=" CG1 VAL 1 928 " pdb=" CG2 VAL 1 928 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE 1 271 " pdb=" CA ILE 1 271 " pdb=" CG1 ILE 1 271 " pdb=" CG2 ILE 1 271 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA PRO B 169 " pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CB PRO B 169 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1307 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 1 951 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO 1 952 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO 1 952 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO 1 952 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 733 " -0.016 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR 1 733 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 733 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 733 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 733 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 733 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR 1 733 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 1 733 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 484 " -0.018 2.00e-02 2.50e+03 1.72e-02 5.19e+00 pdb=" CG PHE 1 484 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 484 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 484 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 484 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 484 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE 1 484 " 0.001 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2343 2.79 - 3.32: 8018 3.32 - 3.85: 13964 3.85 - 4.37: 17024 4.37 - 4.90: 28108 Nonbonded interactions: 69457 Sorted by model distance: nonbonded pdb=" OH TYR 1 902 " pdb=" OE1 GLN 11107 " model vdw 2.269 3.040 nonbonded pdb=" O ILE 1 934 " pdb=" OG1 THR 1 937 " model vdw 2.279 3.040 nonbonded pdb=" CB ALA 1 772 " pdb=" OD2 ASP B 125 " model vdw 2.288 3.460 nonbonded pdb=" O ASP 1 539 " pdb=" OG1 THR 1 542 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR 1 124 " pdb=" O SER 1 345 " model vdw 2.331 3.040 ... (remaining 69452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 0.053 8566 Z= 0.354 Angle : 1.046 14.517 11585 Z= 0.613 Chirality : 0.051 0.327 1310 Planarity : 0.007 0.071 1473 Dihedral : 11.570 75.163 3095 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.70 % Allowed : 5.10 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -5.37 (0.18), residues: 1080 helix: -4.17 (0.10), residues: 573 sheet: -2.86 (0.74), residues: 45 loop : -2.57 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP 1 230 HIS 0.012 0.002 HIS 1 738 PHE 0.038 0.003 PHE 1 484 TYR 0.038 0.002 TYR 1 733 ARG 0.009 0.001 ARG 1 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 319 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 GLU cc_start: 0.8553 (tp30) cc_final: 0.8311 (tp30) REVERT: 1 65 ARG cc_start: 0.7941 (mtt180) cc_final: 0.6839 (mmt180) REVERT: 1 77 GLN cc_start: 0.8595 (tt0) cc_final: 0.8180 (tm-30) REVERT: 1 119 CYS cc_start: 0.8523 (t) cc_final: 0.8042 (m) REVERT: 1 153 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8083 (mtp-110) REVERT: 1 177 SER cc_start: 0.7228 (m) cc_final: 0.6643 (p) REVERT: 1 188 MET cc_start: 0.8325 (ttp) cc_final: 0.7994 (mmt) REVERT: 1 202 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7661 (mm-30) REVERT: 1 203 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8465 (mptt) REVERT: 1 221 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.7798 (tmm160) REVERT: 1 261 LEU cc_start: 0.7733 (tt) cc_final: 0.7475 (tt) REVERT: 1 332 MET cc_start: 0.7759 (tpt) cc_final: 0.7521 (tpp) REVERT: 1 373 ASN cc_start: 0.8700 (t160) cc_final: 0.8442 (t0) REVERT: 1 466 TYR cc_start: 0.7356 (t80) cc_final: 0.6969 (t80) REVERT: 1 480 SER cc_start: 0.8858 (t) cc_final: 0.8619 (p) REVERT: 1 483 HIS cc_start: 0.7389 (t-90) cc_final: 0.6453 (t70) REVERT: 1 522 MET cc_start: 0.8485 (mtp) cc_final: 0.8036 (mtp) REVERT: 1 543 MET cc_start: 0.8333 (mmt) cc_final: 0.7924 (mpp) REVERT: 1 569 GLN cc_start: 0.8461 (tp40) cc_final: 0.7259 (tm-30) REVERT: 1 576 PHE cc_start: 0.7740 (m-10) cc_final: 0.7326 (m-10) REVERT: 1 582 TYR cc_start: 0.8066 (m-10) cc_final: 0.7567 (m-10) REVERT: 1 585 MET cc_start: 0.7534 (mmm) cc_final: 0.6627 (mmp) REVERT: 1 651 TYR cc_start: 0.8134 (m-10) cc_final: 0.7875 (m-10) REVERT: 1 653 GLU cc_start: 0.8857 (tp30) cc_final: 0.8501 (tp30) REVERT: 1 674 TYR cc_start: 0.8118 (t80) cc_final: 0.7439 (t80) REVERT: 1 693 GLU cc_start: 0.8172 (pt0) cc_final: 0.7767 (mt-10) REVERT: 1 768 ASP cc_start: 0.8712 (t0) cc_final: 0.8402 (t70) REVERT: 1 770 MET cc_start: 0.7456 (mmm) cc_final: 0.6810 (ppp) REVERT: 1 803 LYS cc_start: 0.8637 (mttt) cc_final: 0.8418 (mptt) REVERT: 1 876 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8332 (mmtm) REVERT: 1 906 VAL cc_start: 0.7535 (t) cc_final: 0.7235 (t) REVERT: 1 1036 LEU cc_start: 0.8256 (mp) cc_final: 0.7823 (tt) REVERT: 1 1038 MET cc_start: 0.7357 (mmt) cc_final: 0.6807 (mmm) REVERT: 1 1129 VAL cc_start: 0.9068 (t) cc_final: 0.8849 (p) REVERT: B 136 LEU cc_start: 0.8569 (tm) cc_final: 0.8194 (tp) outliers start: 6 outliers final: 0 residues processed: 319 average time/residue: 0.2311 time to fit residues: 96.8614 Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.0370 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 38 GLN 1 58 ASN 1 237 ASN 1 303 HIS 1 338 ASN 1 353 GLN 1 373 ASN 1 383 ASN ** 1 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN 1 686 ASN ** 1 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN 1 818 GLN 1 913 GLN 1 935 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8566 Z= 0.180 Angle : 0.629 9.211 11585 Z= 0.324 Chirality : 0.041 0.154 1310 Planarity : 0.005 0.058 1473 Dihedral : 5.439 27.221 1184 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.78 % Allowed : 13.67 % Favored : 83.55 % 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: -3.49 (0.21), residues: 1080 helix: -2.21 (0.16), residues: 618 sheet: -2.14 (0.71), residues: 50 loop : -2.26 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 230 HIS 0.005 0.001 HIS 1 738 PHE 0.023 0.002 PHE 1 875 TYR 0.018 0.001 TYR 1 961 ARG 0.004 0.001 ARG 1 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 GLU cc_start: 0.8711 (tp30) cc_final: 0.8319 (tp30) REVERT: 1 24 SER cc_start: 0.8470 (t) cc_final: 0.8165 (p) REVERT: 1 56 ASP cc_start: 0.7906 (p0) cc_final: 0.7584 (p0) REVERT: 1 60 LEU cc_start: 0.8979 (tt) cc_final: 0.8541 (tp) REVERT: 1 65 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7118 (mmt-90) REVERT: 1 77 GLN cc_start: 0.8864 (tt0) cc_final: 0.8462 (tm-30) REVERT: 1 119 CYS cc_start: 0.8764 (t) cc_final: 0.7853 (m) REVERT: 1 124 TYR cc_start: 0.7579 (t80) cc_final: 0.7305 (t80) REVERT: 1 156 MET cc_start: 0.8310 (tpt) cc_final: 0.8060 (tpt) REVERT: 1 202 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7846 (mm-30) REVERT: 1 203 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8488 (mmtp) REVERT: 1 221 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.7736 (tmm160) REVERT: 1 314 MET cc_start: 0.8734 (mmm) cc_final: 0.8388 (mmm) REVERT: 1 320 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8333 (tt) REVERT: 1 465 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8364 (mm-30) REVERT: 1 467 MET cc_start: 0.8570 (mmm) cc_final: 0.8245 (mmm) REVERT: 1 480 SER cc_start: 0.8972 (t) cc_final: 0.8741 (m) REVERT: 1 483 HIS cc_start: 0.7252 (t-90) cc_final: 0.6955 (t70) REVERT: 1 492 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6938 (ptp-170) REVERT: 1 522 MET cc_start: 0.8273 (mtp) cc_final: 0.7904 (mtp) REVERT: 1 540 GLU cc_start: 0.8094 (pm20) cc_final: 0.7539 (tm-30) REVERT: 1 550 LEU cc_start: 0.9470 (tp) cc_final: 0.9236 (mt) REVERT: 1 555 TYR cc_start: 0.7557 (m-80) cc_final: 0.7127 (m-80) REVERT: 1 559 ARG cc_start: 0.8699 (ttt-90) cc_final: 0.7841 (ttt-90) REVERT: 1 576 PHE cc_start: 0.7716 (m-10) cc_final: 0.7254 (m-10) REVERT: 1 582 TYR cc_start: 0.8050 (m-10) cc_final: 0.7756 (m-10) REVERT: 1 584 TRP cc_start: 0.8583 (p90) cc_final: 0.8317 (p90) REVERT: 1 585 MET cc_start: 0.7632 (mmm) cc_final: 0.7379 (mmp) REVERT: 1 653 GLU cc_start: 0.8568 (tp30) cc_final: 0.8219 (tp30) REVERT: 1 736 LYS cc_start: 0.8700 (tttt) cc_final: 0.8462 (ttmm) REVERT: 1 746 MET cc_start: 0.8064 (ttm) cc_final: 0.7837 (ttp) REVERT: 1 751 TYR cc_start: 0.8086 (t80) cc_final: 0.7796 (t80) REVERT: 1 803 LYS cc_start: 0.8720 (mttt) cc_final: 0.8455 (mmtt) REVERT: 1 846 MET cc_start: 0.8693 (mmm) cc_final: 0.8235 (mmp) REVERT: 1 866 CYS cc_start: 0.8953 (m) cc_final: 0.8367 (m) REVERT: 1 876 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8336 (mmtm) REVERT: 1 890 MET cc_start: 0.7447 (mmm) cc_final: 0.7211 (mmm) REVERT: 1 942 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7757 (tm-30) REVERT: 1 958 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7226 (tp-100) REVERT: 1 961 TYR cc_start: 0.7530 (t80) cc_final: 0.7170 (t80) REVERT: 1 977 MET cc_start: 0.8490 (tpt) cc_final: 0.8082 (tpt) REVERT: 1 1021 MET cc_start: 0.8107 (ptm) cc_final: 0.6955 (ppp) REVERT: 1 1034 ILE cc_start: 0.7765 (mt) cc_final: 0.7563 (mt) REVERT: 1 1036 LEU cc_start: 0.8426 (mp) cc_final: 0.8190 (tt) REVERT: 1 1038 MET cc_start: 0.7841 (mmt) cc_final: 0.7453 (mmp) REVERT: 1 1065 LYS cc_start: 0.7368 (pttp) cc_final: 0.7028 (mtmm) REVERT: 1 1091 ASP cc_start: 0.8514 (t0) cc_final: 0.8076 (t0) REVERT: B 136 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (tp) outliers start: 24 outliers final: 12 residues processed: 287 average time/residue: 0.2028 time to fit residues: 78.8679 Evaluate side-chains 240 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 263 SER Chi-restraints excluded: chain 1 residue 320 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 955 ILE Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 1 77 GLN 1 303 HIS 1 485 ASN 1 517 ASN 1 573 GLN 1 644 ASN 1 705 HIS 1 713 GLN 1 750 HIS 1 910 HIS ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8566 Z= 0.231 Angle : 0.628 10.375 11585 Z= 0.317 Chirality : 0.041 0.139 1310 Planarity : 0.005 0.062 1473 Dihedral : 5.102 27.522 1184 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.06 % Allowed : 15.76 % Favored : 80.19 % 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: -1.94 (0.24), residues: 1080 helix: -0.88 (0.19), residues: 608 sheet: -0.99 (0.83), residues: 45 loop : -1.78 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 1 288 HIS 0.006 0.001 HIS 1 738 PHE 0.021 0.002 PHE 1 922 TYR 0.020 0.002 TYR 1 138 ARG 0.003 0.000 ARG 1 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 246 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 18 GLU cc_start: 0.8591 (tp30) cc_final: 0.8216 (tp30) REVERT: 1 24 SER cc_start: 0.8150 (t) cc_final: 0.7897 (p) REVERT: 1 65 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7328 (mmt180) REVERT: 1 77 GLN cc_start: 0.8727 (tt0) cc_final: 0.8280 (tm-30) REVERT: 1 156 MET cc_start: 0.8330 (tpt) cc_final: 0.7801 (tpt) REVERT: 1 188 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7937 (tpt) REVERT: 1 202 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7821 (mm-30) REVERT: 1 221 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7698 (tmm160) REVERT: 1 264 ASP cc_start: 0.7567 (t0) cc_final: 0.7129 (t0) REVERT: 1 345 SER cc_start: 0.9322 (t) cc_final: 0.8892 (p) REVERT: 1 467 MET cc_start: 0.8839 (mmm) cc_final: 0.8550 (mmm) REVERT: 1 480 SER cc_start: 0.8984 (t) cc_final: 0.8645 (m) REVERT: 1 482 LYS cc_start: 0.8511 (tmtp) cc_final: 0.7976 (tptp) REVERT: 1 483 HIS cc_start: 0.7290 (t-90) cc_final: 0.6923 (t-170) REVERT: 1 519 ILE cc_start: 0.7854 (mm) cc_final: 0.7509 (mm) REVERT: 1 540 GLU cc_start: 0.8117 (pm20) cc_final: 0.7423 (tm-30) REVERT: 1 555 TYR cc_start: 0.7873 (m-80) cc_final: 0.7449 (m-80) REVERT: 1 559 ARG cc_start: 0.8759 (ttt-90) cc_final: 0.8022 (ttt-90) REVERT: 1 570 LEU cc_start: 0.8863 (mt) cc_final: 0.8534 (mp) REVERT: 1 576 PHE cc_start: 0.7610 (m-80) cc_final: 0.7252 (m-10) REVERT: 1 582 TYR cc_start: 0.8044 (m-10) cc_final: 0.7325 (m-10) REVERT: 1 585 MET cc_start: 0.7670 (mmm) cc_final: 0.7145 (mmt) REVERT: 1 633 GLU cc_start: 0.8060 (tp30) cc_final: 0.7661 (pp20) REVERT: 1 650 LEU cc_start: 0.8009 (mp) cc_final: 0.7604 (mp) REVERT: 1 653 GLU cc_start: 0.8686 (tp30) cc_final: 0.8386 (tp30) REVERT: 1 702 MET cc_start: 0.7800 (mmp) cc_final: 0.7583 (mmp) REVERT: 1 707 ARG cc_start: 0.8410 (tmt170) cc_final: 0.8170 (tpt90) REVERT: 1 751 TYR cc_start: 0.8209 (t80) cc_final: 0.7886 (t80) REVERT: 1 803 LYS cc_start: 0.8588 (mttt) cc_final: 0.8303 (mmtt) REVERT: 1 846 MET cc_start: 0.8494 (mmm) cc_final: 0.7397 (mmm) REVERT: 1 866 CYS cc_start: 0.9035 (m) cc_final: 0.8569 (m) REVERT: 1 890 MET cc_start: 0.7449 (mmm) cc_final: 0.7159 (mmm) REVERT: 1 906 VAL cc_start: 0.7249 (t) cc_final: 0.7049 (t) REVERT: 1 935 HIS cc_start: 0.7687 (m170) cc_final: 0.7347 (m-70) REVERT: 1 942 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7837 (tm-30) REVERT: 1 958 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7642 (tp40) REVERT: 1 961 TYR cc_start: 0.7401 (t80) cc_final: 0.7095 (t80) REVERT: 1 964 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6188 (mt) REVERT: 1 977 MET cc_start: 0.8527 (tpt) cc_final: 0.8145 (tpt) REVERT: 1 1021 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.6796 (ppp) REVERT: 1 1034 ILE cc_start: 0.7816 (mt) cc_final: 0.7602 (mt) REVERT: 1 1036 LEU cc_start: 0.8437 (mp) cc_final: 0.8141 (tt) REVERT: 1 1091 ASP cc_start: 0.8557 (t0) cc_final: 0.8126 (t0) REVERT: 1 1131 MET cc_start: 0.6297 (ptm) cc_final: 0.5992 (ttp) outliers start: 35 outliers final: 17 residues processed: 261 average time/residue: 0.2072 time to fit residues: 73.1701 Evaluate side-chains 234 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 188 MET Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 458 LEU Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 955 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1016 SER Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 51 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 311 HIS 1 513 ASN ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8566 Z= 0.182 Angle : 0.595 9.079 11585 Z= 0.298 Chirality : 0.040 0.163 1310 Planarity : 0.004 0.060 1473 Dihedral : 4.797 26.880 1184 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.17 % Allowed : 16.92 % Favored : 78.91 % 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: -1.11 (0.25), residues: 1080 helix: -0.09 (0.20), residues: 613 sheet: -0.45 (0.87), residues: 45 loop : -1.66 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 1 288 HIS 0.005 0.001 HIS 1 738 PHE 0.021 0.002 PHE 1 123 TYR 0.016 0.001 TYR 1 138 ARG 0.004 0.000 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 32 GLU cc_start: 0.8443 (tp30) cc_final: 0.8032 (mm-30) REVERT: 1 65 ARG cc_start: 0.8568 (mtt180) cc_final: 0.7523 (mmt180) REVERT: 1 77 GLN cc_start: 0.8724 (tt0) cc_final: 0.8276 (tm-30) REVERT: 1 156 MET cc_start: 0.8141 (tpt) cc_final: 0.7845 (tpt) REVERT: 1 188 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7823 (tpt) REVERT: 1 202 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7812 (mm-30) REVERT: 1 221 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.7679 (tmm160) REVERT: 1 264 ASP cc_start: 0.7635 (t0) cc_final: 0.7291 (t0) REVERT: 1 288 TRP cc_start: 0.5404 (t-100) cc_final: 0.5136 (t-100) REVERT: 1 345 SER cc_start: 0.9286 (t) cc_final: 0.8815 (p) REVERT: 1 388 ASN cc_start: 0.6582 (OUTLIER) cc_final: 0.6280 (p0) REVERT: 1 467 MET cc_start: 0.8784 (mmm) cc_final: 0.8099 (mmm) REVERT: 1 480 SER cc_start: 0.9004 (t) cc_final: 0.8566 (p) REVERT: 1 482 LYS cc_start: 0.8529 (tmtp) cc_final: 0.8081 (tptp) REVERT: 1 483 HIS cc_start: 0.7168 (t-90) cc_final: 0.6694 (t-90) REVERT: 1 519 ILE cc_start: 0.7704 (mm) cc_final: 0.7146 (mp) REVERT: 1 540 GLU cc_start: 0.8067 (pm20) cc_final: 0.7438 (tm-30) REVERT: 1 555 TYR cc_start: 0.8016 (m-80) cc_final: 0.7507 (m-80) REVERT: 1 559 ARG cc_start: 0.8670 (ttt-90) cc_final: 0.7888 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8441 (tp40) cc_final: 0.7650 (tm-30) REVERT: 1 570 LEU cc_start: 0.8844 (mt) cc_final: 0.8630 (mp) REVERT: 1 582 TYR cc_start: 0.8004 (m-10) cc_final: 0.7343 (m-10) REVERT: 1 585 MET cc_start: 0.7791 (mmm) cc_final: 0.7386 (mmt) REVERT: 1 633 GLU cc_start: 0.8134 (tp30) cc_final: 0.7710 (pp20) REVERT: 1 653 GLU cc_start: 0.8709 (tp30) cc_final: 0.8437 (tp30) REVERT: 1 674 TYR cc_start: 0.7502 (t80) cc_final: 0.7145 (t80) REVERT: 1 707 ARG cc_start: 0.8399 (tmt170) cc_final: 0.8181 (tpt90) REVERT: 1 751 TYR cc_start: 0.8085 (t80) cc_final: 0.7729 (t80) REVERT: 1 758 MET cc_start: 0.8391 (mmm) cc_final: 0.8125 (mmp) REVERT: 1 803 LYS cc_start: 0.8712 (mttt) cc_final: 0.8435 (mmtt) REVERT: 1 846 MET cc_start: 0.8565 (mmm) cc_final: 0.8330 (mmp) REVERT: 1 890 MET cc_start: 0.7428 (mmm) cc_final: 0.7114 (mmm) REVERT: 1 892 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7553 (mt0) REVERT: 1 906 VAL cc_start: 0.7021 (t) cc_final: 0.6819 (t) REVERT: 1 935 HIS cc_start: 0.7555 (m170) cc_final: 0.7305 (m-70) REVERT: 1 961 TYR cc_start: 0.7474 (t80) cc_final: 0.7229 (t80) REVERT: 1 964 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6337 (mt) REVERT: 1 977 MET cc_start: 0.8495 (tpt) cc_final: 0.8150 (tpt) REVERT: 1 1021 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.6902 (ppp) REVERT: 1 1034 ILE cc_start: 0.7657 (mt) cc_final: 0.7438 (mt) REVERT: 1 1036 LEU cc_start: 0.8543 (mp) cc_final: 0.8192 (tt) REVERT: 1 1091 ASP cc_start: 0.8500 (t0) cc_final: 0.8119 (t0) REVERT: 1 1131 MET cc_start: 0.6106 (ptm) cc_final: 0.5859 (ttp) REVERT: B 123 GLU cc_start: 0.5762 (tp30) cc_final: 0.5402 (tp30) outliers start: 36 outliers final: 22 residues processed: 250 average time/residue: 0.1926 time to fit residues: 66.7345 Evaluate side-chains 239 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 188 MET Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 320 LEU Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 449 VAL Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 1 303 HIS 1 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8566 Z= 0.252 Angle : 0.628 7.937 11585 Z= 0.316 Chirality : 0.041 0.147 1310 Planarity : 0.004 0.063 1473 Dihedral : 4.836 28.067 1184 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.17 % Allowed : 17.96 % Favored : 77.87 % 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: -0.83 (0.25), residues: 1080 helix: 0.17 (0.21), residues: 613 sheet: -1.00 (0.83), residues: 50 loop : -1.49 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 986 HIS 0.005 0.001 HIS 1 738 PHE 0.023 0.002 PHE 1 123 TYR 0.019 0.002 TYR 1 674 ARG 0.005 0.001 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 32 GLU cc_start: 0.8588 (tp30) cc_final: 0.7953 (mm-30) REVERT: 1 65 ARG cc_start: 0.8602 (mtt180) cc_final: 0.7638 (mmt180) REVERT: 1 77 GLN cc_start: 0.8831 (tt0) cc_final: 0.8340 (tm-30) REVERT: 1 202 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7761 (mm-30) REVERT: 1 221 ARG cc_start: 0.8421 (tpp-160) cc_final: 0.7651 (tmm160) REVERT: 1 264 ASP cc_start: 0.7744 (t0) cc_final: 0.7358 (t0) REVERT: 1 274 LEU cc_start: 0.7742 (mt) cc_final: 0.7498 (mm) REVERT: 1 345 SER cc_start: 0.9330 (t) cc_final: 0.8871 (p) REVERT: 1 465 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8402 (mm-30) REVERT: 1 466 TYR cc_start: 0.7914 (t80) cc_final: 0.7295 (t80) REVERT: 1 467 MET cc_start: 0.8701 (mmm) cc_final: 0.8179 (mmm) REVERT: 1 480 SER cc_start: 0.8981 (t) cc_final: 0.8528 (p) REVERT: 1 482 LYS cc_start: 0.8590 (tmtp) cc_final: 0.8079 (tptp) REVERT: 1 483 HIS cc_start: 0.7254 (t-90) cc_final: 0.6851 (t-90) REVERT: 1 540 GLU cc_start: 0.8056 (pm20) cc_final: 0.7381 (tm-30) REVERT: 1 555 TYR cc_start: 0.8039 (m-80) cc_final: 0.7573 (m-80) REVERT: 1 559 ARG cc_start: 0.8698 (ttt-90) cc_final: 0.7960 (ttt-90) REVERT: 1 570 LEU cc_start: 0.8812 (mt) cc_final: 0.8513 (mp) REVERT: 1 582 TYR cc_start: 0.7965 (m-10) cc_final: 0.7264 (m-10) REVERT: 1 585 MET cc_start: 0.7894 (mmm) cc_final: 0.7259 (mmp) REVERT: 1 633 GLU cc_start: 0.8202 (tp30) cc_final: 0.7746 (pp20) REVERT: 1 653 GLU cc_start: 0.8806 (tp30) cc_final: 0.8603 (tp30) REVERT: 1 702 MET cc_start: 0.7414 (mmp) cc_final: 0.6742 (mmm) REVERT: 1 707 ARG cc_start: 0.8443 (tmt170) cc_final: 0.8100 (tpt90) REVERT: 1 758 MET cc_start: 0.8403 (mmm) cc_final: 0.8186 (mmp) REVERT: 1 892 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7666 (mt0) REVERT: 1 961 TYR cc_start: 0.7514 (t80) cc_final: 0.7247 (t80) REVERT: 1 964 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6069 (mt) REVERT: 1 977 MET cc_start: 0.8527 (tpt) cc_final: 0.8176 (tpt) REVERT: 1 1021 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.6891 (ppp) REVERT: 1 1036 LEU cc_start: 0.8559 (mp) cc_final: 0.8235 (tt) REVERT: 1 1091 ASP cc_start: 0.8784 (t0) cc_final: 0.8284 (t0) REVERT: 1 1106 ARG cc_start: 0.6325 (mmt-90) cc_final: 0.5907 (mmp80) REVERT: 1 1109 SER cc_start: 0.8039 (p) cc_final: 0.7622 (p) REVERT: 1 1112 MET cc_start: 0.7847 (mmt) cc_final: 0.7624 (mmm) REVERT: 1 1131 MET cc_start: 0.6443 (ptm) cc_final: 0.6072 (ttp) outliers start: 36 outliers final: 27 residues processed: 237 average time/residue: 0.1999 time to fit residues: 65.4926 Evaluate side-chains 228 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 188 MET Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 458 LEU Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 862 ILE Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1137 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.0060 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN ** 1 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8566 Z= 0.194 Angle : 0.609 8.304 11585 Z= 0.303 Chirality : 0.040 0.154 1310 Planarity : 0.004 0.062 1473 Dihedral : 4.698 26.604 1184 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.71 % Allowed : 20.16 % Favored : 76.13 % 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: -0.42 (0.26), residues: 1080 helix: 0.48 (0.21), residues: 609 sheet: -0.03 (0.93), residues: 40 loop : -1.35 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 288 HIS 0.005 0.001 HIS 1 738 PHE 0.023 0.002 PHE 1 546 TYR 0.014 0.001 TYR 1 138 ARG 0.005 0.000 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7836 (ttp80) REVERT: 1 32 GLU cc_start: 0.8454 (tp30) cc_final: 0.7967 (mm-30) REVERT: 1 58 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7710 (t0) REVERT: 1 65 ARG cc_start: 0.8568 (mtt180) cc_final: 0.7620 (mmt180) REVERT: 1 77 GLN cc_start: 0.8847 (tt0) cc_final: 0.8361 (tm-30) REVERT: 1 202 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7747 (mm-30) REVERT: 1 221 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.7640 (tmm160) REVERT: 1 388 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.6224 (p0) REVERT: 1 465 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8405 (mm-30) REVERT: 1 466 TYR cc_start: 0.7863 (t80) cc_final: 0.7063 (t80) REVERT: 1 467 MET cc_start: 0.8684 (mmm) cc_final: 0.8213 (mmm) REVERT: 1 480 SER cc_start: 0.8926 (t) cc_final: 0.8516 (p) REVERT: 1 482 LYS cc_start: 0.8625 (tmtp) cc_final: 0.7968 (tptp) REVERT: 1 483 HIS cc_start: 0.7223 (t-90) cc_final: 0.6804 (t-90) REVERT: 1 540 GLU cc_start: 0.8207 (pm20) cc_final: 0.7583 (tm-30) REVERT: 1 555 TYR cc_start: 0.7954 (m-80) cc_final: 0.7452 (m-80) REVERT: 1 559 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.7983 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8428 (tp40) cc_final: 0.7707 (tm-30) REVERT: 1 570 LEU cc_start: 0.8785 (mt) cc_final: 0.8490 (mp) REVERT: 1 582 TYR cc_start: 0.7888 (m-10) cc_final: 0.7322 (m-10) REVERT: 1 585 MET cc_start: 0.7891 (mmm) cc_final: 0.7181 (mmp) REVERT: 1 631 ARG cc_start: 0.7266 (mtt-85) cc_final: 0.6949 (ttm110) REVERT: 1 633 GLU cc_start: 0.8200 (tp30) cc_final: 0.7723 (pp20) REVERT: 1 639 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6585 (ttm) REVERT: 1 653 GLU cc_start: 0.8824 (tp30) cc_final: 0.8525 (tp30) REVERT: 1 702 MET cc_start: 0.7361 (mmp) cc_final: 0.6911 (mmp) REVERT: 1 770 MET cc_start: 0.7882 (mmp) cc_final: 0.7488 (ppp) REVERT: 1 795 MET cc_start: 0.8587 (tmm) cc_final: 0.8216 (tmm) REVERT: 1 892 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7674 (mt0) REVERT: 1 961 TYR cc_start: 0.7542 (t80) cc_final: 0.7263 (t80) REVERT: 1 964 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.6046 (mt) REVERT: 1 977 MET cc_start: 0.8470 (tpt) cc_final: 0.8109 (tpt) REVERT: 1 1021 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.6863 (ppp) REVERT: 1 1091 ASP cc_start: 0.8793 (t0) cc_final: 0.8331 (t0) REVERT: 1 1106 ARG cc_start: 0.6305 (mmt-90) cc_final: 0.5938 (mmp80) REVERT: 1 1112 MET cc_start: 0.8019 (mmt) cc_final: 0.7800 (mmm) REVERT: 1 1131 MET cc_start: 0.6412 (ptm) cc_final: 0.6020 (ttp) outliers start: 32 outliers final: 18 residues processed: 232 average time/residue: 0.1940 time to fit residues: 61.9570 Evaluate side-chains 227 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 263 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 639 MET Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 87 optimal weight: 0.0060 chunk 58 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 517 ASN 1 713 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8566 Z= 0.168 Angle : 0.600 8.830 11585 Z= 0.300 Chirality : 0.039 0.135 1310 Planarity : 0.004 0.060 1473 Dihedral : 4.546 25.576 1184 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.71 % Allowed : 21.32 % Favored : 74.97 % 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: -0.12 (0.26), residues: 1080 helix: 0.74 (0.21), residues: 612 sheet: -0.73 (0.88), residues: 45 loop : -1.16 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 288 HIS 0.004 0.001 HIS 1 738 PHE 0.019 0.002 PHE 1 123 TYR 0.024 0.001 TYR 1 674 ARG 0.006 0.000 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7808 (ttp80) REVERT: 1 32 GLU cc_start: 0.8426 (tp30) cc_final: 0.7972 (mm-30) REVERT: 1 58 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7723 (t0) REVERT: 1 65 ARG cc_start: 0.8510 (mtt180) cc_final: 0.7475 (mmt180) REVERT: 1 77 GLN cc_start: 0.8992 (tt0) cc_final: 0.8003 (tm-30) REVERT: 1 202 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7719 (mm-30) REVERT: 1 221 ARG cc_start: 0.8434 (tpp-160) cc_final: 0.7638 (tmm160) REVERT: 1 388 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.6019 (p0) REVERT: 1 466 TYR cc_start: 0.7854 (t80) cc_final: 0.6994 (t80) REVERT: 1 467 MET cc_start: 0.8807 (mmm) cc_final: 0.8369 (mmm) REVERT: 1 480 SER cc_start: 0.8934 (t) cc_final: 0.8508 (p) REVERT: 1 482 LYS cc_start: 0.8550 (tmtp) cc_final: 0.7865 (tptp) REVERT: 1 483 HIS cc_start: 0.6953 (t-90) cc_final: 0.6729 (t-90) REVERT: 1 540 GLU cc_start: 0.8180 (pm20) cc_final: 0.7546 (tm-30) REVERT: 1 555 TYR cc_start: 0.7891 (m-80) cc_final: 0.7462 (m-80) REVERT: 1 569 GLN cc_start: 0.8424 (tp40) cc_final: 0.7570 (tm-30) REVERT: 1 570 LEU cc_start: 0.8788 (mt) cc_final: 0.8514 (mp) REVERT: 1 582 TYR cc_start: 0.7957 (m-10) cc_final: 0.7402 (m-10) REVERT: 1 585 MET cc_start: 0.7950 (mmm) cc_final: 0.7270 (mmp) REVERT: 1 631 ARG cc_start: 0.7284 (mtt-85) cc_final: 0.6917 (ttm110) REVERT: 1 633 GLU cc_start: 0.8188 (tp30) cc_final: 0.7689 (pp20) REVERT: 1 653 GLU cc_start: 0.8738 (tp30) cc_final: 0.8477 (tp30) REVERT: 1 763 PHE cc_start: 0.7917 (t80) cc_final: 0.7162 (m-80) REVERT: 1 770 MET cc_start: 0.8080 (mmp) cc_final: 0.7616 (ppp) REVERT: 1 795 MET cc_start: 0.8577 (tmm) cc_final: 0.8207 (tmm) REVERT: 1 892 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7688 (mt0) REVERT: 1 961 TYR cc_start: 0.7053 (t80) cc_final: 0.6845 (t80) REVERT: 1 964 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5680 (mt) REVERT: 1 977 MET cc_start: 0.8416 (tpt) cc_final: 0.8052 (tpt) REVERT: 1 1021 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7133 (ppp) REVERT: 1 1084 PHE cc_start: 0.7766 (t80) cc_final: 0.7549 (t80) REVERT: 1 1091 ASP cc_start: 0.8780 (t0) cc_final: 0.8314 (t0) REVERT: 1 1106 ARG cc_start: 0.6486 (mmt-90) cc_final: 0.6014 (mmp80) REVERT: 1 1109 SER cc_start: 0.7953 (p) cc_final: 0.7525 (p) REVERT: 1 1131 MET cc_start: 0.6417 (ptm) cc_final: 0.6032 (ttp) REVERT: B 126 MET cc_start: 0.6842 (ttp) cc_final: 0.6595 (ttm) outliers start: 32 outliers final: 18 residues processed: 237 average time/residue: 0.2019 time to fit residues: 66.5863 Evaluate side-chains 233 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 263 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN ** 1 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8566 Z= 0.185 Angle : 0.620 9.604 11585 Z= 0.308 Chirality : 0.040 0.134 1310 Planarity : 0.004 0.054 1473 Dihedral : 4.523 24.774 1184 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.36 % Allowed : 21.67 % Favored : 74.97 % 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: -0.03 (0.26), residues: 1080 helix: 0.80 (0.21), residues: 614 sheet: -0.62 (0.88), residues: 45 loop : -1.13 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 1 858 HIS 0.003 0.001 HIS 1 738 PHE 0.027 0.002 PHE 1 546 TYR 0.019 0.001 TYR 1 138 ARG 0.006 0.000 ARG 1 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7802 (ttp80) REVERT: 1 32 GLU cc_start: 0.8434 (tp30) cc_final: 0.7954 (mm-30) REVERT: 1 58 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7670 (t0) REVERT: 1 65 ARG cc_start: 0.8515 (mtt180) cc_final: 0.7474 (mmt180) REVERT: 1 77 GLN cc_start: 0.9007 (tt0) cc_final: 0.8123 (tm-30) REVERT: 1 202 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7709 (mm-30) REVERT: 1 221 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.7639 (tmm160) REVERT: 1 388 ASN cc_start: 0.6349 (OUTLIER) cc_final: 0.6126 (p0) REVERT: 1 466 TYR cc_start: 0.7870 (t80) cc_final: 0.6943 (t80) REVERT: 1 467 MET cc_start: 0.8818 (mmm) cc_final: 0.8433 (mmm) REVERT: 1 480 SER cc_start: 0.8955 (t) cc_final: 0.8518 (p) REVERT: 1 482 LYS cc_start: 0.8583 (tmtp) cc_final: 0.7895 (tptp) REVERT: 1 540 GLU cc_start: 0.8178 (pm20) cc_final: 0.7547 (tm-30) REVERT: 1 552 ILE cc_start: 0.8979 (mt) cc_final: 0.8713 (mt) REVERT: 1 555 TYR cc_start: 0.7870 (m-80) cc_final: 0.7398 (m-80) REVERT: 1 559 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7766 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8444 (tp40) cc_final: 0.7617 (tm-30) REVERT: 1 570 LEU cc_start: 0.8823 (mt) cc_final: 0.8522 (mp) REVERT: 1 582 TYR cc_start: 0.7966 (m-10) cc_final: 0.7421 (m-10) REVERT: 1 585 MET cc_start: 0.7972 (mmm) cc_final: 0.7314 (mmp) REVERT: 1 631 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.6953 (ttm110) REVERT: 1 633 GLU cc_start: 0.8194 (tp30) cc_final: 0.7685 (pp20) REVERT: 1 653 GLU cc_start: 0.8774 (tp30) cc_final: 0.8512 (tp30) REVERT: 1 685 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.6779 (mtm-85) REVERT: 1 702 MET cc_start: 0.7284 (mmp) cc_final: 0.6759 (mmm) REVERT: 1 763 PHE cc_start: 0.7908 (t80) cc_final: 0.7165 (m-80) REVERT: 1 770 MET cc_start: 0.8093 (mmp) cc_final: 0.7623 (ppp) REVERT: 1 795 MET cc_start: 0.8587 (tmm) cc_final: 0.8213 (tmm) REVERT: 1 892 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7700 (mt0) REVERT: 1 961 TYR cc_start: 0.7097 (t80) cc_final: 0.6887 (t80) REVERT: 1 964 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5697 (mt) REVERT: 1 977 MET cc_start: 0.8409 (tpt) cc_final: 0.8011 (tpt) REVERT: 1 1021 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.6865 (ppp) REVERT: 1 1023 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7811 (tpt90) REVERT: 1 1084 PHE cc_start: 0.7784 (t80) cc_final: 0.7209 (t80) REVERT: 1 1091 ASP cc_start: 0.8797 (t0) cc_final: 0.8331 (t0) REVERT: 1 1109 SER cc_start: 0.7920 (p) cc_final: 0.7611 (p) outliers start: 29 outliers final: 21 residues processed: 231 average time/residue: 0.1938 time to fit residues: 62.2548 Evaluate side-chains 231 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 263 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 320 LEU Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS 1 517 ASN 1 713 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8566 Z= 0.218 Angle : 0.635 11.412 11585 Z= 0.317 Chirality : 0.040 0.145 1310 Planarity : 0.004 0.052 1473 Dihedral : 4.580 25.406 1184 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.59 % Allowed : 22.02 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1080 helix: 0.81 (0.21), residues: 614 sheet: -0.60 (0.87), residues: 45 loop : -1.14 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 858 HIS 0.004 0.001 HIS 1 483 PHE 0.035 0.002 PHE 1 546 TYR 0.025 0.002 TYR 1 674 ARG 0.006 0.000 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: 1 32 GLU cc_start: 0.8397 (tp30) cc_final: 0.8094 (mm-30) REVERT: 1 58 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7711 (t0) REVERT: 1 65 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7426 (mmt180) REVERT: 1 77 GLN cc_start: 0.9017 (tt0) cc_final: 0.8336 (tm-30) REVERT: 1 180 MET cc_start: 0.8596 (tmm) cc_final: 0.8180 (tmm) REVERT: 1 202 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7762 (mm-30) REVERT: 1 221 ARG cc_start: 0.8480 (tpp-160) cc_final: 0.7703 (tmm160) REVERT: 1 388 ASN cc_start: 0.6296 (OUTLIER) cc_final: 0.6032 (p0) REVERT: 1 466 TYR cc_start: 0.7816 (t80) cc_final: 0.6949 (t80) REVERT: 1 480 SER cc_start: 0.8964 (t) cc_final: 0.8533 (p) REVERT: 1 482 LYS cc_start: 0.8600 (tmtp) cc_final: 0.8007 (tptp) REVERT: 1 552 ILE cc_start: 0.8912 (mt) cc_final: 0.8660 (mt) REVERT: 1 555 TYR cc_start: 0.7698 (m-80) cc_final: 0.7253 (m-80) REVERT: 1 569 GLN cc_start: 0.8460 (tp40) cc_final: 0.7690 (tm-30) REVERT: 1 582 TYR cc_start: 0.7944 (m-10) cc_final: 0.7410 (m-10) REVERT: 1 585 MET cc_start: 0.8064 (mmm) cc_final: 0.7443 (mmp) REVERT: 1 631 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.7040 (ttm110) REVERT: 1 633 GLU cc_start: 0.8214 (tp30) cc_final: 0.7693 (pp20) REVERT: 1 639 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6888 (mtt) REVERT: 1 653 GLU cc_start: 0.8785 (tp30) cc_final: 0.8501 (tp30) REVERT: 1 702 MET cc_start: 0.7246 (mmp) cc_final: 0.6859 (mmm) REVERT: 1 795 MET cc_start: 0.8605 (tmm) cc_final: 0.8237 (tmm) REVERT: 1 892 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7617 (mt0) REVERT: 1 961 TYR cc_start: 0.7077 (t80) cc_final: 0.6845 (t80) REVERT: 1 964 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5754 (mt) REVERT: 1 977 MET cc_start: 0.8361 (tpt) cc_final: 0.8017 (tpt) REVERT: 1 1021 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.6901 (ppp) REVERT: 1 1091 ASP cc_start: 0.8572 (t0) cc_final: 0.8208 (t0) outliers start: 31 outliers final: 22 residues processed: 225 average time/residue: 0.1957 time to fit residues: 63.1696 Evaluate side-chains 231 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 263 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 639 MET Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1066 CYS Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 0.0050 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8566 Z= 0.184 Angle : 0.634 11.519 11585 Z= 0.314 Chirality : 0.040 0.136 1310 Planarity : 0.004 0.052 1473 Dihedral : 4.503 24.604 1184 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.01 % Allowed : 22.71 % Favored : 74.28 % 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: 0.06 (0.26), residues: 1080 helix: 0.88 (0.21), residues: 612 sheet: -0.44 (0.87), residues: 45 loop : -1.11 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 858 HIS 0.003 0.001 HIS 1 738 PHE 0.020 0.002 PHE 1 123 TYR 0.025 0.001 TYR 1 751 ARG 0.005 0.000 ARG 1 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7527 (ttp80) REVERT: 1 32 GLU cc_start: 0.8405 (tp30) cc_final: 0.8118 (mm-30) REVERT: 1 58 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7625 (t0) REVERT: 1 65 ARG cc_start: 0.8448 (mtt180) cc_final: 0.7287 (mmt180) REVERT: 1 77 GLN cc_start: 0.9008 (tt0) cc_final: 0.8132 (tm-30) REVERT: 1 202 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7703 (mm-30) REVERT: 1 221 ARG cc_start: 0.8478 (tpp-160) cc_final: 0.7706 (tmm160) REVERT: 1 466 TYR cc_start: 0.7611 (t80) cc_final: 0.6929 (t80) REVERT: 1 468 MET cc_start: 0.8712 (tpt) cc_final: 0.8413 (tpt) REVERT: 1 480 SER cc_start: 0.8947 (t) cc_final: 0.8416 (p) REVERT: 1 482 LYS cc_start: 0.8479 (tmtp) cc_final: 0.7790 (tptp) REVERT: 1 552 ILE cc_start: 0.8899 (mt) cc_final: 0.8644 (mt) REVERT: 1 555 TYR cc_start: 0.7517 (m-80) cc_final: 0.7154 (m-80) REVERT: 1 569 GLN cc_start: 0.8417 (tp40) cc_final: 0.7556 (tm-30) REVERT: 1 582 TYR cc_start: 0.7893 (m-10) cc_final: 0.7361 (m-10) REVERT: 1 585 MET cc_start: 0.8079 (mmm) cc_final: 0.7318 (mmp) REVERT: 1 631 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.7129 (ttm110) REVERT: 1 633 GLU cc_start: 0.8151 (tp30) cc_final: 0.7627 (pp20) REVERT: 1 639 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6531 (mtm) REVERT: 1 653 GLU cc_start: 0.8758 (tp30) cc_final: 0.8472 (tp30) REVERT: 1 726 MET cc_start: 0.8323 (mtp) cc_final: 0.8020 (mtm) REVERT: 1 758 MET cc_start: 0.8245 (mmm) cc_final: 0.8013 (mmp) REVERT: 1 763 PHE cc_start: 0.7903 (t80) cc_final: 0.7148 (m-80) REVERT: 1 770 MET cc_start: 0.8100 (mmp) cc_final: 0.7635 (ppp) REVERT: 1 795 MET cc_start: 0.8585 (tmm) cc_final: 0.8206 (tmm) REVERT: 1 892 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7623 (mt0) REVERT: 1 977 MET cc_start: 0.8273 (tpt) cc_final: 0.7958 (tpt) REVERT: 1 1021 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.6856 (ppp) REVERT: 1 1023 ARG cc_start: 0.8091 (tpt90) cc_final: 0.7819 (tpt90) REVERT: 1 1091 ASP cc_start: 0.8732 (t0) cc_final: 0.8340 (t0) REVERT: 1 1112 MET cc_start: 0.7927 (mmm) cc_final: 0.7717 (mmm) outliers start: 26 outliers final: 21 residues processed: 220 average time/residue: 0.2277 time to fit residues: 69.3448 Evaluate side-chains 226 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 123 PHE Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 263 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 639 MET Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1066 CYS Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN 1 713 GLN ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120575 restraints weight = 14229.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123726 restraints weight = 8398.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125940 restraints weight = 5637.614| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8566 Z= 0.191 Angle : 0.655 13.731 11585 Z= 0.322 Chirality : 0.040 0.134 1310 Planarity : 0.004 0.053 1473 Dihedral : 4.489 24.623 1184 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.24 % Allowed : 22.71 % Favored : 74.04 % 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: 0.12 (0.26), residues: 1080 helix: 0.93 (0.21), residues: 612 sheet: -0.27 (0.87), residues: 45 loop : -1.10 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 858 HIS 0.004 0.001 HIS 1 935 PHE 0.033 0.002 PHE 1 546 TYR 0.030 0.002 TYR 1 961 ARG 0.006 0.000 ARG 1 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.07 seconds wall clock time: 39 minutes 18.26 seconds (2358.26 seconds total)