Starting phenix.real_space_refine on Thu Feb 13 00:21:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mz6_3583/02_2025/5mz6_3583.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mz6_3583/02_2025/5mz6_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/cci-nas-00/data/ceres_data/5mz6_3583/02_2025/5mz6_3583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mz6_3583/02_2025/5mz6_3583.map" model { file = "/net/cci-nas-00/data/ceres_data/5mz6_3583/02_2025/5mz6_3583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mz6_3583/02_2025/5mz6_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.56, per 1000 atoms: 0.54 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: 1.88 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: 0.96 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: 2.24 Time building geometry restraints manager: 2.22 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: 0.390 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.120 Find NCS groups from input model: 0.070 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 6 poor density : 319 time to evaluate : 1.016 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: 0.2426 time to fit residues: 101.5069 Evaluate side-chains 216 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123176 restraints weight = 14261.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126387 restraints weight = 8250.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128643 restraints weight = 5514.661| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 SER cc_start: 0.9170 (t) cc_final: 0.8789 (p) REVERT: 1 60 LEU cc_start: 0.9128 (tt) cc_final: 0.8871 (tp) REVERT: 1 65 ARG cc_start: 0.7431 (mtt180) cc_final: 0.6933 (mmt-90) REVERT: 1 124 TYR cc_start: 0.7753 (t80) cc_final: 0.7538 (t80) REVERT: 1 203 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8397 (mmtp) REVERT: 1 314 MET cc_start: 0.8902 (mmm) cc_final: 0.8594 (mmm) REVERT: 1 320 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8498 (tt) REVERT: 1 465 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8211 (mm-30) REVERT: 1 492 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.7238 (ptp-170) REVERT: 1 522 MET cc_start: 0.8693 (mtp) cc_final: 0.8400 (mtp) REVERT: 1 540 GLU cc_start: 0.7604 (pm20) cc_final: 0.7347 (tm-30) REVERT: 1 550 LEU cc_start: 0.9160 (tp) cc_final: 0.8948 (mt) REVERT: 1 559 ARG cc_start: 0.8828 (ttt-90) cc_final: 0.8130 (ttt-90) REVERT: 1 573 GLN cc_start: 0.8799 (tt0) cc_final: 0.8597 (tt0) REVERT: 1 576 PHE cc_start: 0.7916 (m-10) cc_final: 0.7506 (m-10) REVERT: 1 736 LYS cc_start: 0.8993 (tttt) cc_final: 0.8772 (ttmm) REVERT: 1 846 MET cc_start: 0.8624 (mmm) cc_final: 0.8222 (mmp) REVERT: 1 890 MET cc_start: 0.8011 (mmm) cc_final: 0.7735 (mmm) REVERT: 1 961 TYR cc_start: 0.8197 (t80) cc_final: 0.7923 (t80) REVERT: 1 1021 MET cc_start: 0.7582 (ptm) cc_final: 0.7066 (ppp) REVERT: 1 1036 LEU cc_start: 0.8849 (mp) cc_final: 0.8521 (tt) REVERT: 1 1091 ASP cc_start: 0.8025 (t0) cc_final: 0.7808 (t0) outliers start: 24 outliers final: 12 residues processed: 287 average time/residue: 0.2220 time to fit residues: 86.1251 Evaluate side-chains 226 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 1 483 HIS 1 485 ASN ** 1 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN 1 644 ASN 1 705 HIS 1 713 GLN 1 910 HIS 1 935 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119478 restraints weight = 14530.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122661 restraints weight = 8418.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124841 restraints weight = 5617.525| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8566 Z= 0.215 Angle : 0.631 10.532 11585 Z= 0.318 Chirality : 0.041 0.133 1310 Planarity : 0.005 0.065 1473 Dihedral : 5.046 27.288 1184 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.17 % Allowed : 16.34 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.24), residues: 1080 helix: -0.94 (0.19), residues: 614 sheet: -0.98 (0.83), residues: 45 loop : -1.82 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 584 HIS 0.005 0.001 HIS 1 738 PHE 0.019 0.002 PHE 1 922 TYR 0.019 0.002 TYR 1 138 ARG 0.003 0.000 ARG 1 378 *********************** 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 271 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 SER cc_start: 0.8954 (t) cc_final: 0.8625 (p) REVERT: 1 65 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7213 (mmt180) REVERT: 1 188 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6447 (tpt) REVERT: 1 519 ILE cc_start: 0.8709 (mm) cc_final: 0.8050 (mm) REVERT: 1 540 GLU cc_start: 0.7655 (pm20) cc_final: 0.7383 (tm-30) REVERT: 1 559 ARG cc_start: 0.8821 (ttt-90) cc_final: 0.8179 (ttt-90) REVERT: 1 570 LEU cc_start: 0.8999 (mt) cc_final: 0.8766 (mp) REVERT: 1 573 GLN cc_start: 0.8788 (tt0) cc_final: 0.8574 (tt0) REVERT: 1 576 PHE cc_start: 0.7829 (m-80) cc_final: 0.7352 (m-10) REVERT: 1 585 MET cc_start: 0.7474 (mmp) cc_final: 0.6617 (mmp) REVERT: 1 650 LEU cc_start: 0.8445 (mp) cc_final: 0.8129 (mp) REVERT: 1 846 MET cc_start: 0.8474 (mmm) cc_final: 0.7675 (mmm) REVERT: 1 890 MET cc_start: 0.8033 (mmm) cc_final: 0.7678 (mmm) REVERT: 1 961 TYR cc_start: 0.8090 (t80) cc_final: 0.7804 (t80) REVERT: 1 1021 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7088 (ppp) REVERT: 1 1036 LEU cc_start: 0.8860 (mp) cc_final: 0.8454 (tt) REVERT: 1 1131 MET cc_start: 0.6930 (ptm) cc_final: 0.6453 (ttp) outliers start: 36 outliers final: 19 residues processed: 252 average time/residue: 0.2111 time to fit residues: 72.7611 Evaluate side-chains 221 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 302 VAL 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 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 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 57 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 303 HIS ** 1 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118535 restraints weight = 14238.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121708 restraints weight = 8366.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123869 restraints weight = 5679.536| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8566 Z= 0.211 Angle : 0.614 8.721 11585 Z= 0.311 Chirality : 0.041 0.166 1310 Planarity : 0.004 0.068 1473 Dihedral : 4.884 26.531 1184 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.40 % Allowed : 18.08 % Favored : 77.52 % 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: -1.27 (0.25), residues: 1080 helix: -0.24 (0.20), residues: 611 sheet: -0.65 (0.85), residues: 45 loop : -1.66 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 1 288 HIS 0.011 0.001 HIS 1 483 PHE 0.021 0.002 PHE 1 123 TYR 0.016 0.001 TYR 1 138 ARG 0.003 0.000 ARG 1 130 *********************** 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 247 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7225 (mmt180) REVERT: 1 465 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8139 (mm-30) REVERT: 1 467 MET cc_start: 0.7952 (mmm) cc_final: 0.7716 (mmm) REVERT: 1 519 ILE cc_start: 0.8657 (mm) cc_final: 0.8094 (mt) REVERT: 1 540 GLU cc_start: 0.7596 (pm20) cc_final: 0.7274 (tm-30) REVERT: 1 559 ARG cc_start: 0.8775 (ttt-90) cc_final: 0.8080 (ttt-90) REVERT: 1 573 GLN cc_start: 0.8802 (tt0) cc_final: 0.8587 (tt0) REVERT: 1 585 MET cc_start: 0.7552 (mmp) cc_final: 0.6723 (mmp) REVERT: 1 674 TYR cc_start: 0.7848 (t80) cc_final: 0.7635 (t80) REVERT: 1 726 MET cc_start: 0.7853 (mtp) cc_final: 0.7639 (mtm) REVERT: 1 890 MET cc_start: 0.8061 (mmm) cc_final: 0.7694 (mmm) REVERT: 1 892 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7401 (mt0) REVERT: 1 961 TYR cc_start: 0.8038 (t80) cc_final: 0.7782 (t80) REVERT: 1 964 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6151 (mt) REVERT: 1 1021 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7119 (ppp) REVERT: B 123 GLU cc_start: 0.6247 (tp30) cc_final: 0.5673 (tp30) outliers start: 38 outliers final: 22 residues processed: 228 average time/residue: 0.2069 time to fit residues: 65.5960 Evaluate side-chains 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN 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 276 SER Chi-restraints excluded: chain 1 residue 302 VAL 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 903 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 1 513 ASN 1 517 ASN ** 1 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120065 restraints weight = 14144.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123276 restraints weight = 8220.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125485 restraints weight = 5478.717| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4370 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= 0.191 Angle : 0.600 7.870 11585 Z= 0.302 Chirality : 0.040 0.145 1310 Planarity : 0.004 0.066 1473 Dihedral : 4.724 27.130 1184 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.87 % Allowed : 18.08 % Favored : 77.06 % 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: -0.79 (0.25), residues: 1080 helix: 0.15 (0.20), residues: 622 sheet: -0.13 (0.94), residues: 40 loop : -1.52 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 738 PHE 0.023 0.002 PHE 1 123 TYR 0.020 0.001 TYR 1 674 ARG 0.004 0.000 ARG 1 130 *********************** 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 246 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7188 (mmt180) REVERT: 1 388 ASN cc_start: 0.6122 (OUTLIER) cc_final: 0.5887 (p0) REVERT: 1 519 ILE cc_start: 0.8722 (mm) cc_final: 0.8160 (mt) REVERT: 1 559 ARG cc_start: 0.8786 (ttt-90) cc_final: 0.8130 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8924 (tp40) cc_final: 0.8719 (tp40) REVERT: 1 573 GLN cc_start: 0.8706 (tt0) cc_final: 0.8439 (tt0) REVERT: 1 751 TYR cc_start: 0.7814 (t80) cc_final: 0.7608 (t80) REVERT: 1 890 MET cc_start: 0.8038 (mmm) cc_final: 0.7657 (mmm) REVERT: 1 892 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7437 (mt0) REVERT: 1 964 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6177 (mt) REVERT: 1 1021 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7075 (ppp) outliers start: 42 outliers final: 26 residues processed: 227 average time/residue: 0.2088 time to fit residues: 65.0293 Evaluate side-chains 219 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 302 VAL 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 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 650 LEU Chi-restraints excluded: chain 1 residue 713 GLN 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 1016 SER 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 B residue 122 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119066 restraints weight = 14266.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122096 restraints weight = 8419.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124259 restraints weight = 5712.512| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8566 Z= 0.214 Angle : 0.627 10.256 11585 Z= 0.315 Chirality : 0.041 0.147 1310 Planarity : 0.004 0.067 1473 Dihedral : 4.744 27.103 1184 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.82 % Allowed : 19.93 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1080 helix: 0.33 (0.21), residues: 621 sheet: -0.04 (0.93), residues: 40 loop : -1.46 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 986 HIS 0.005 0.001 HIS 1 738 PHE 0.027 0.002 PHE 1 576 TYR 0.033 0.002 TYR 1 961 ARG 0.005 0.000 ARG 1 329 *********************** 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 231 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7215 (mmt180) REVERT: 1 388 ASN cc_start: 0.6221 (OUTLIER) cc_final: 0.5947 (p0) REVERT: 1 519 ILE cc_start: 0.8878 (mm) cc_final: 0.8310 (mp) REVERT: 1 559 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.8135 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8889 (tp40) cc_final: 0.8665 (tp40) REVERT: 1 573 GLN cc_start: 0.8722 (tt0) cc_final: 0.8424 (tt0) REVERT: 1 585 MET cc_start: 0.7447 (mmp) cc_final: 0.6605 (mmp) REVERT: 1 751 TYR cc_start: 0.7972 (t80) cc_final: 0.7696 (t80) REVERT: 1 795 MET cc_start: 0.8115 (tmm) cc_final: 0.7842 (ppp) REVERT: 1 890 MET cc_start: 0.8059 (mmm) cc_final: 0.7687 (mmm) REVERT: 1 892 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7065 (mt0) REVERT: 1 964 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6222 (mt) REVERT: 1 1021 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7021 (ppp) REVERT: 1 1036 LEU cc_start: 0.9039 (mp) cc_final: 0.8592 (tt) REVERT: B 138 GLU cc_start: 0.8480 (pm20) cc_final: 0.8230 (pm20) outliers start: 33 outliers final: 25 residues processed: 214 average time/residue: 0.2025 time to fit residues: 59.3611 Evaluate side-chains 207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL 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 276 SER Chi-restraints excluded: chain 1 residue 302 VAL 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 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 726 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 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1137 VAL 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 105 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 52 ASN 1 517 ASN 1 713 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120209 restraints weight = 14306.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123290 restraints weight = 8477.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125450 restraints weight = 5739.067| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8566 Z= 0.190 Angle : 0.616 10.151 11585 Z= 0.308 Chirality : 0.040 0.163 1310 Planarity : 0.004 0.066 1473 Dihedral : 4.639 26.345 1184 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.48 % Allowed : 21.55 % 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: -0.26 (0.26), residues: 1080 helix: 0.59 (0.21), residues: 615 sheet: -0.03 (0.91), residues: 40 loop : -1.26 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 738 PHE 0.028 0.002 PHE 1 576 TYR 0.024 0.001 TYR 1 961 ARG 0.010 0.000 ARG 1 329 *********************** 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 228 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7350 (mmt180) REVERT: 1 388 ASN cc_start: 0.6161 (OUTLIER) cc_final: 0.5925 (p0) REVERT: 1 466 TYR cc_start: 0.7895 (t80) cc_final: 0.7512 (t80) REVERT: 1 519 ILE cc_start: 0.8671 (mm) cc_final: 0.8123 (mp) REVERT: 1 569 GLN cc_start: 0.8777 (tp40) cc_final: 0.8563 (tp40) REVERT: 1 573 GLN cc_start: 0.8767 (tt0) cc_final: 0.8466 (tt0) REVERT: 1 795 MET cc_start: 0.8181 (tmm) cc_final: 0.7879 (ppp) REVERT: 1 890 MET cc_start: 0.8030 (mmm) cc_final: 0.7639 (mmm) REVERT: 1 892 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7075 (mt0) REVERT: 1 964 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6066 (mt) REVERT: 1 1021 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6932 (ppp) REVERT: 1 1036 LEU cc_start: 0.8947 (mp) cc_final: 0.8561 (tt) outliers start: 30 outliers final: 19 residues processed: 214 average time/residue: 0.1986 time to fit residues: 59.1223 Evaluate side-chains 206 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 52 ASN Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 302 VAL 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 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 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 B residue 122 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS ** 1 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN ** 1 548 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.132731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116632 restraints weight = 14521.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119639 restraints weight = 8676.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121728 restraints weight = 5908.532| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8566 Z= 0.228 Angle : 0.659 15.836 11585 Z= 0.327 Chirality : 0.041 0.140 1310 Planarity : 0.004 0.067 1473 Dihedral : 4.699 25.716 1184 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.48 % Allowed : 21.78 % Favored : 74.74 % 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: -0.21 (0.26), residues: 1080 helix: 0.64 (0.21), residues: 614 sheet: -0.03 (0.90), residues: 40 loop : -1.25 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 858 HIS 0.004 0.001 HIS 1 738 PHE 0.031 0.002 PHE 1 576 TYR 0.024 0.002 TYR 1 674 ARG 0.007 0.001 ARG 1 329 *********************** 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 219 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7329 (mmt-90) REVERT: 1 388 ASN cc_start: 0.6074 (OUTLIER) cc_final: 0.5830 (p0) REVERT: 1 466 TYR cc_start: 0.8331 (t80) cc_final: 0.7871 (t80) REVERT: 1 519 ILE cc_start: 0.8568 (mm) cc_final: 0.8286 (mm) REVERT: 1 569 GLN cc_start: 0.8796 (tp40) cc_final: 0.8557 (tp40) REVERT: 1 573 GLN cc_start: 0.8788 (tt0) cc_final: 0.8522 (tt0) REVERT: 1 631 ARG cc_start: 0.6563 (ttm110) cc_final: 0.6299 (ttm110) REVERT: 1 651 TYR cc_start: 0.8356 (m-10) cc_final: 0.8142 (m-10) REVERT: 1 795 MET cc_start: 0.8269 (tmm) cc_final: 0.7936 (ppp) REVERT: 1 890 MET cc_start: 0.8055 (mmm) cc_final: 0.7668 (mmm) REVERT: 1 892 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7100 (mt0) REVERT: 1 964 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6193 (mt) REVERT: 1 1021 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.6956 (ppp) REVERT: 1 1036 LEU cc_start: 0.8934 (mp) cc_final: 0.8501 (tt) REVERT: B 128 ASN cc_start: 0.6362 (p0) cc_final: 0.6106 (p0) outliers start: 30 outliers final: 23 residues processed: 205 average time/residue: 0.2063 time to fit residues: 59.9508 Evaluate side-chains 207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL 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 276 SER Chi-restraints excluded: chain 1 residue 302 VAL 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 726 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 1137 VAL Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116599 restraints weight = 14642.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119637 restraints weight = 8713.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121750 restraints weight = 5945.732| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8566 Z= 0.232 Angle : 0.683 16.400 11585 Z= 0.337 Chirality : 0.042 0.157 1310 Planarity : 0.004 0.064 1473 Dihedral : 4.710 25.468 1184 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.13 % Allowed : 22.48 % 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: -0.14 (0.26), residues: 1080 helix: 0.72 (0.21), residues: 607 sheet: 0.04 (0.90), residues: 40 loop : -1.23 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 858 HIS 0.004 0.001 HIS 1 738 PHE 0.037 0.002 PHE 1 546 TYR 0.020 0.002 TYR 1 961 ARG 0.007 0.000 ARG 1 130 *********************** 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 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7319 (mmt-90) REVERT: 1 156 MET cc_start: 0.7902 (tpt) cc_final: 0.7661 (mmm) REVERT: 1 388 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.5949 (p0) REVERT: 1 466 TYR cc_start: 0.8011 (t80) cc_final: 0.7407 (t80) REVERT: 1 519 ILE cc_start: 0.8700 (mm) cc_final: 0.8355 (mm) REVERT: 1 569 GLN cc_start: 0.8755 (tp40) cc_final: 0.8500 (tp40) REVERT: 1 573 GLN cc_start: 0.8794 (tt0) cc_final: 0.8480 (tt0) REVERT: 1 631 ARG cc_start: 0.6574 (ttm110) cc_final: 0.6362 (ttm110) REVERT: 1 795 MET cc_start: 0.8306 (tmm) cc_final: 0.7981 (ppp) REVERT: 1 890 MET cc_start: 0.8060 (mmm) cc_final: 0.7665 (mmm) REVERT: 1 892 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7493 (mt0) REVERT: 1 917 GLU cc_start: 0.5943 (pp20) cc_final: 0.5689 (pp20) REVERT: 1 964 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6258 (mt) REVERT: 1 1021 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7012 (ppp) REVERT: 1 1036 LEU cc_start: 0.8907 (mp) cc_final: 0.8518 (tt) outliers start: 27 outliers final: 22 residues processed: 201 average time/residue: 0.1854 time to fit residues: 52.7328 Evaluate side-chains 204 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 SER Chi-restraints excluded: chain 1 residue 302 VAL 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 726 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 1137 VAL Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 935 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118264 restraints weight = 14379.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121242 restraints weight = 8567.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123321 restraints weight = 5812.162| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8566 Z= 0.202 Angle : 0.666 15.773 11585 Z= 0.328 Chirality : 0.041 0.159 1310 Planarity : 0.004 0.060 1473 Dihedral : 4.628 24.734 1184 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.13 % Allowed : 22.60 % 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: -0.08 (0.26), residues: 1080 helix: 0.76 (0.21), residues: 611 sheet: 0.12 (0.90), residues: 40 loop : -1.23 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 154 HIS 0.003 0.001 HIS 1 738 PHE 0.021 0.002 PHE 1 123 TYR 0.026 0.002 TYR 1 674 ARG 0.007 0.001 ARG 1 130 ********************** 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 213 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7263 (mmt-90) REVERT: 1 388 ASN cc_start: 0.6115 (OUTLIER) cc_final: 0.5910 (p0) REVERT: 1 466 TYR cc_start: 0.8051 (t80) cc_final: 0.7639 (t80) REVERT: 1 519 ILE cc_start: 0.8499 (mm) cc_final: 0.8054 (mp) REVERT: 1 569 GLN cc_start: 0.8641 (tp40) cc_final: 0.8402 (tp40) REVERT: 1 573 GLN cc_start: 0.8758 (tt0) cc_final: 0.8461 (tt0) REVERT: 1 578 MET cc_start: 0.7800 (mmp) cc_final: 0.7571 (mmp) REVERT: 1 631 ARG cc_start: 0.6821 (ttm110) cc_final: 0.6552 (ttm110) REVERT: 1 795 MET cc_start: 0.8241 (tmm) cc_final: 0.7912 (ppp) REVERT: 1 890 MET cc_start: 0.8013 (mmm) cc_final: 0.7616 (mmm) REVERT: 1 892 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7495 (mt0) REVERT: 1 964 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6221 (mt) REVERT: 1 1021 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6929 (ppp) outliers start: 27 outliers final: 21 residues processed: 198 average time/residue: 0.1879 time to fit residues: 52.8540 Evaluate side-chains 205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 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 726 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 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1066 CYS Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 15 optimal weight: 0.0170 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 ** 1 802 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.135340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119033 restraints weight = 14535.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122167 restraints weight = 8512.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124317 restraints weight = 5753.872| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8566 Z= 0.193 Angle : 0.673 16.372 11585 Z= 0.328 Chirality : 0.041 0.151 1310 Planarity : 0.004 0.051 1473 Dihedral : 4.538 24.292 1184 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.78 % Allowed : 22.71 % Favored : 74.51 % 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: -0.00 (0.26), residues: 1080 helix: 0.79 (0.21), residues: 617 sheet: 0.29 (0.90), residues: 40 loop : -1.16 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 935 PHE 0.020 0.002 PHE 1 123 TYR 0.017 0.001 TYR 1 961 ARG 0.007 0.001 ARG 1 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.18 seconds wall clock time: 47 minutes 25.23 seconds (2845.23 seconds total)