Starting phenix.real_space_refine on Thu Mar 13 01:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mz6_3583/03_2025/5mz6_3583.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mz6_3583/03_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_3583/03_2025/5mz6_3583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mz6_3583/03_2025/5mz6_3583.map" model { file = "/net/cci-nas-00/data/ceres_data/5mz6_3583/03_2025/5mz6_3583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mz6_3583/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8401 Number of models: 1 Model: "" Number of chains: 2 Chain: "1" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7968 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 32, 'TRANS': 985} Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 433 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 5.30, per 1000 atoms: 0.63 Number of scatterers: 8401 At special positions: 0 Unit cell: (88.66, 124.41, 74.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1535 8.00 N 1457 7.00 C 5339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 11031 " - pdb=" SG CYS 11066 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.1 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: 0.81 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: 2.29 Time building geometry restraints manager: 2.56 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: 0.360 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.220 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- 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 : 0.994 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: 0.2629 time to fit residues: 110.0069 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 : 1.109 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3700 r_free = 0.3700 target = 0.139023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123073 restraints weight = 14232.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126318 restraints weight = 8135.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128598 restraints weight = 5400.337| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 SER cc_start: 0.9168 (t) cc_final: 0.8786 (p) REVERT: 1 60 LEU cc_start: 0.9136 (tt) cc_final: 0.8875 (tp) REVERT: 1 65 ARG cc_start: 0.7453 (mtt180) cc_final: 0.6938 (mmt-90) REVERT: 1 124 TYR cc_start: 0.7756 (t80) cc_final: 0.7538 (t80) REVERT: 1 203 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8399 (mmtp) REVERT: 1 314 MET cc_start: 0.8909 (mmm) cc_final: 0.8598 (mmm) REVERT: 1 320 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8503 (tt) REVERT: 1 465 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8222 (mm-30) REVERT: 1 492 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.7238 (ptp-170) REVERT: 1 522 MET cc_start: 0.8695 (mtp) cc_final: 0.8400 (mtp) REVERT: 1 540 GLU cc_start: 0.7613 (pm20) cc_final: 0.7353 (tm-30) REVERT: 1 550 LEU cc_start: 0.9172 (tp) cc_final: 0.8957 (mt) REVERT: 1 559 ARG cc_start: 0.8831 (ttt-90) cc_final: 0.8130 (ttt-90) REVERT: 1 573 GLN cc_start: 0.8805 (tt0) cc_final: 0.8603 (tt0) REVERT: 1 576 PHE cc_start: 0.7920 (m-10) cc_final: 0.7505 (m-10) REVERT: 1 736 LYS cc_start: 0.8995 (tttt) cc_final: 0.8771 (ttmm) REVERT: 1 846 MET cc_start: 0.8632 (mmm) cc_final: 0.8227 (mmp) REVERT: 1 890 MET cc_start: 0.8007 (mmm) cc_final: 0.7729 (mmm) REVERT: 1 961 TYR cc_start: 0.8196 (t80) cc_final: 0.7921 (t80) REVERT: 1 1021 MET cc_start: 0.7581 (ptm) cc_final: 0.7061 (ppp) REVERT: 1 1036 LEU cc_start: 0.8849 (mp) cc_final: 0.8522 (tt) REVERT: 1 1091 ASP cc_start: 0.8036 (t0) cc_final: 0.7815 (t0) outliers start: 24 outliers final: 12 residues processed: 287 average time/residue: 0.2119 time to fit residues: 82.2955 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 : 1.005 ------------------------------------------------------------------------------- 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: 0.8980 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 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 = 0.3651 r_free = 0.3651 target = 0.135185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119095 restraints weight = 14557.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122295 restraints weight = 8482.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124514 restraints weight = 5680.528| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8566 Z= 0.220 Angle : 0.633 10.516 11585 Z= 0.320 Chirality : 0.041 0.133 1310 Planarity : 0.005 0.066 1473 Dihedral : 5.063 27.256 1184 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.06 % Allowed : 16.45 % 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: -1.00 (0.83), residues: 45 loop : -1.81 (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 269 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 SER cc_start: 0.9090 (t) cc_final: 0.8756 (p) REVERT: 1 65 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7219 (mmt180) REVERT: 1 188 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6701 (tpt) REVERT: 1 519 ILE cc_start: 0.8714 (mm) cc_final: 0.8074 (mm) REVERT: 1 540 GLU cc_start: 0.7649 (pm20) cc_final: 0.7375 (tm-30) REVERT: 1 559 ARG cc_start: 0.8819 (ttt-90) cc_final: 0.8175 (ttt-90) REVERT: 1 570 LEU cc_start: 0.9001 (mt) cc_final: 0.8771 (mp) REVERT: 1 573 GLN cc_start: 0.8772 (tt0) cc_final: 0.8550 (tt0) REVERT: 1 576 PHE cc_start: 0.7840 (m-80) cc_final: 0.7366 (m-10) REVERT: 1 585 MET cc_start: 0.7468 (mmp) cc_final: 0.6605 (mmp) REVERT: 1 650 LEU cc_start: 0.8470 (mp) cc_final: 0.8156 (mp) REVERT: 1 751 TYR cc_start: 0.8208 (t80) cc_final: 0.7998 (t80) REVERT: 1 846 MET cc_start: 0.8447 (mmm) cc_final: 0.7660 (mmm) REVERT: 1 890 MET cc_start: 0.8043 (mmm) cc_final: 0.7689 (mmm) REVERT: 1 961 TYR cc_start: 0.8099 (t80) cc_final: 0.7817 (t80) REVERT: 1 1021 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7098 (ppp) REVERT: 1 1036 LEU cc_start: 0.8864 (mp) cc_final: 0.8469 (tt) REVERT: 1 1091 ASP cc_start: 0.8065 (t0) cc_final: 0.7859 (t0) REVERT: 1 1131 MET cc_start: 0.6934 (ptm) cc_final: 0.6440 (ttp) outliers start: 35 outliers final: 19 residues processed: 251 average time/residue: 0.2194 time to fit residues: 77.4032 Evaluate side-chains 224 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 0.0870 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 1 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120064 restraints weight = 14194.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123210 restraints weight = 8292.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125405 restraints weight = 5607.019| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8566 Z= 0.187 Angle : 0.604 9.342 11585 Z= 0.304 Chirality : 0.040 0.163 1310 Planarity : 0.004 0.066 1473 Dihedral : 4.830 26.546 1184 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.17 % Allowed : 18.54 % Favored : 77.29 % 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: -1.23 (0.25), residues: 1080 helix: -0.22 (0.20), residues: 613 sheet: -0.61 (0.85), residues: 45 loop : -1.63 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 288 HIS 0.011 0.001 HIS 1 483 PHE 0.019 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 253 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7173 (mmt180) REVERT: 1 156 MET cc_start: 0.7857 (tpt) cc_final: 0.7608 (tpt) REVERT: 1 227 TYR cc_start: 0.8693 (t80) cc_final: 0.8457 (t80) REVERT: 1 388 ASN cc_start: 0.6243 (OUTLIER) cc_final: 0.6004 (p0) REVERT: 1 465 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8069 (mm-30) REVERT: 1 519 ILE cc_start: 0.8667 (mm) cc_final: 0.8123 (mt) REVERT: 1 540 GLU cc_start: 0.7485 (pm20) cc_final: 0.7220 (tm-30) REVERT: 1 559 ARG cc_start: 0.8768 (ttt-90) cc_final: 0.8119 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8920 (tp40) cc_final: 0.8214 (tm-30) REVERT: 1 573 GLN cc_start: 0.8763 (tt0) cc_final: 0.8557 (tt0) REVERT: 1 674 TYR cc_start: 0.7884 (t80) cc_final: 0.7674 (t80) REVERT: 1 890 MET cc_start: 0.8057 (mmm) cc_final: 0.7692 (mmm) REVERT: 1 892 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7372 (mt0) REVERT: 1 961 TYR cc_start: 0.8066 (t80) cc_final: 0.7828 (t80) REVERT: 1 964 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6136 (mt) REVERT: 1 1021 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7105 (ppp) REVERT: 1 1091 ASP cc_start: 0.7992 (t0) cc_final: 0.7741 (t0) REVERT: B 123 GLU cc_start: 0.6079 (tp30) cc_final: 0.5534 (tp30) outliers start: 36 outliers final: 20 residues processed: 236 average time/residue: 0.1845 time to fit residues: 60.7103 Evaluate side-chains 225 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 320 LEU 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 921 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE 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: 0.9980 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 311 HIS 1 517 ASN ** 1 940 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 = 0.3647 r_free = 0.3647 target = 0.134805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118351 restraints weight = 14201.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121434 restraints weight = 8397.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123564 restraints weight = 5735.770| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8566 Z= 0.218 Angle : 0.615 8.104 11585 Z= 0.311 Chirality : 0.041 0.155 1310 Planarity : 0.004 0.068 1473 Dihedral : 4.778 27.868 1184 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.29 % Allowed : 19.24 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1080 helix: 0.10 (0.21), residues: 618 sheet: -0.79 (0.89), residues: 45 loop : -1.43 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 288 HIS 0.006 0.001 HIS 1 483 PHE 0.023 0.002 PHE 1 123 TYR 0.019 0.001 TYR 1 674 ARG 0.004 0.000 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7242 (mmt180) REVERT: 1 388 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.5916 (p0) REVERT: 1 465 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7912 (mm-30) REVERT: 1 519 ILE cc_start: 0.8744 (mm) cc_final: 0.8166 (mt) REVERT: 1 559 ARG cc_start: 0.8780 (ttt-90) cc_final: 0.8133 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8951 (tp40) cc_final: 0.8284 (tm-30) REVERT: 1 573 GLN cc_start: 0.8735 (tt0) cc_final: 0.8531 (tt0) REVERT: 1 751 TYR cc_start: 0.7968 (t80) cc_final: 0.7704 (t80) REVERT: 1 795 MET cc_start: 0.8166 (tmm) cc_final: 0.7954 (tmm) REVERT: 1 890 MET cc_start: 0.8053 (mmm) cc_final: 0.7689 (mmm) REVERT: 1 892 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7538 (mt0) REVERT: 1 961 TYR cc_start: 0.8163 (t80) cc_final: 0.7932 (t80) REVERT: 1 964 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6151 (mt) REVERT: 1 1021 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7042 (ppp) REVERT: 1 1036 LEU cc_start: 0.8996 (mp) cc_final: 0.8530 (tt) REVERT: 1 1091 ASP cc_start: 0.8143 (t0) cc_final: 0.7822 (t0) outliers start: 37 outliers final: 23 residues processed: 219 average time/residue: 0.2117 time to fit residues: 63.6031 Evaluate side-chains 216 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 726 MET Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1137 VAL Chi-restraints excluded: chain B residue 122 ILE 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: 0.0010 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122074 restraints weight = 14160.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125203 restraints weight = 8180.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127471 restraints weight = 5464.005| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4556 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= 0.176 Angle : 0.623 10.113 11585 Z= 0.308 Chirality : 0.040 0.139 1310 Planarity : 0.004 0.065 1473 Dihedral : 4.654 26.066 1184 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.36 % Allowed : 20.63 % Favored : 76.01 % 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: -0.57 (0.25), residues: 1080 helix: 0.31 (0.21), residues: 623 sheet: -0.06 (0.91), residues: 40 loop : -1.40 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 PHE 0.028 0.002 PHE 1 576 TYR 0.024 0.001 TYR 1 674 ARG 0.006 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 243 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7149 (mmt180) REVERT: 1 519 ILE cc_start: 0.8617 (mm) cc_final: 0.8102 (mp) REVERT: 1 573 GLN cc_start: 0.8729 (tt0) cc_final: 0.8459 (tt0) REVERT: 1 751 TYR cc_start: 0.8154 (t80) cc_final: 0.7872 (t80) REVERT: 1 890 MET cc_start: 0.8017 (mmm) cc_final: 0.7623 (mmm) REVERT: 1 892 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7532 (mt0) REVERT: 1 922 PHE cc_start: 0.8539 (m-80) cc_final: 0.8331 (m-10) REVERT: 1 964 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6101 (mt) REVERT: 1 1021 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7040 (ppp) REVERT: 1 1036 LEU cc_start: 0.8865 (mp) cc_final: 0.8527 (tt) REVERT: 1 1091 ASP cc_start: 0.8046 (t0) cc_final: 0.7769 (t0) outliers start: 29 outliers final: 21 residues processed: 224 average time/residue: 0.2072 time to fit residues: 63.3587 Evaluate side-chains 215 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 726 MET Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR 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 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 chunk 6 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 0.1948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN ** 1 689 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.139980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123582 restraints weight = 14158.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126789 restraints weight = 8310.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129041 restraints weight = 5597.211| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8566 Z= 0.164 Angle : 0.618 9.766 11585 Z= 0.308 Chirality : 0.039 0.150 1310 Planarity : 0.004 0.063 1473 Dihedral : 4.461 24.963 1184 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.78 % Allowed : 22.13 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1080 helix: 0.58 (0.21), residues: 623 sheet: -0.33 (0.88), residues: 45 loop : -1.24 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 1 154 HIS 0.003 0.001 HIS 1 483 PHE 0.027 0.002 PHE 1 576 TYR 0.028 0.001 TYR 1 961 ARG 0.005 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 238 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7144 (mmt180) REVERT: 1 75 TYR cc_start: 0.6784 (m-80) cc_final: 0.6452 (m-80) REVERT: 1 378 ARG cc_start: 0.8379 (ptm-80) cc_final: 0.8160 (ptm-80) REVERT: 1 519 ILE cc_start: 0.8519 (mm) cc_final: 0.8087 (mt) REVERT: 1 631 ARG cc_start: 0.6586 (ttm110) cc_final: 0.6345 (ttm110) REVERT: 1 702 MET cc_start: 0.6478 (mmp) cc_final: 0.6036 (mmm) REVERT: 1 795 MET cc_start: 0.8017 (tmm) cc_final: 0.7718 (ppp) REVERT: 1 890 MET cc_start: 0.7942 (mmm) cc_final: 0.7515 (mmm) REVERT: 1 892 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7457 (mt0) REVERT: 1 1021 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6963 (ppp) REVERT: 1 1084 PHE cc_start: 0.7834 (t80) cc_final: 0.7607 (t80) outliers start: 24 outliers final: 16 residues processed: 223 average time/residue: 0.2122 time to fit residues: 65.7008 Evaluate side-chains 214 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 155 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 377 MET Chi-restraints excluded: chain 1 residue 449 VAL Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE 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: 1.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 80 optimal weight: 0.3980 chunk 87 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN ** 1 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11048 GLN ** 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 = 0.3727 r_free = 0.3727 target = 0.140438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123392 restraints weight = 14496.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126544 restraints weight = 8709.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128779 restraints weight = 5992.041| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8566 Z= 0.177 Angle : 0.632 10.532 11585 Z= 0.316 Chirality : 0.039 0.148 1310 Planarity : 0.004 0.057 1473 Dihedral : 4.415 24.447 1184 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.20 % Allowed : 22.94 % Favored : 74.86 % 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: -0.09 (0.26), residues: 1080 helix: 0.65 (0.21), residues: 623 sheet: 0.67 (0.89), residues: 40 loop : -1.17 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 986 HIS 0.004 0.001 HIS 1 483 PHE 0.032 0.002 PHE 1 546 TYR 0.024 0.001 TYR 1 674 ARG 0.005 0.000 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 225 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7182 (mmt-90) REVERT: 1 378 ARG cc_start: 0.8413 (ptm-80) cc_final: 0.8176 (ptm-80) REVERT: 1 519 ILE cc_start: 0.8379 (mm) cc_final: 0.8003 (mt) REVERT: 1 631 ARG cc_start: 0.6564 (ttm110) cc_final: 0.6244 (ttm110) REVERT: 1 639 MET cc_start: 0.8251 (tpp) cc_final: 0.6776 (ttm) REVERT: 1 793 ARG cc_start: 0.7666 (ttt180) cc_final: 0.6126 (ttm110) REVERT: 1 795 MET cc_start: 0.8093 (tmm) cc_final: 0.7773 (ppp) REVERT: 1 890 MET cc_start: 0.7953 (mmm) cc_final: 0.7514 (mmm) REVERT: 1 892 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7553 (mt0) REVERT: 1 1021 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.6996 (ppp) outliers start: 19 outliers final: 14 residues processed: 214 average time/residue: 0.2352 time to fit residues: 68.8573 Evaluate side-chains 207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 137 ASP 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 449 VAL Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 650 LEU Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 1016 SER Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1066 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN ** 11048 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119390 restraints weight = 14631.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122477 restraints weight = 8743.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124641 restraints weight = 6026.829| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8566 Z= 0.231 Angle : 0.694 13.046 11585 Z= 0.343 Chirality : 0.041 0.184 1310 Planarity : 0.004 0.057 1473 Dihedral : 4.547 24.987 1184 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.20 % Allowed : 23.17 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1080 helix: 0.60 (0.21), residues: 624 sheet: -0.09 (0.87), residues: 45 loop : -1.05 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 986 HIS 0.004 0.001 HIS 1 935 PHE 0.030 0.002 PHE 1 576 TYR 0.014 0.001 TYR 1 961 ARG 0.006 0.000 ARG 1 707 *********************** 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 214 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7280 (mmt-90) REVERT: 1 378 ARG cc_start: 0.8414 (ptm-80) cc_final: 0.8146 (ptm-80) REVERT: 1 519 ILE cc_start: 0.8435 (mm) cc_final: 0.8006 (mp) REVERT: 1 631 ARG cc_start: 0.6674 (ttm110) cc_final: 0.6463 (ttm110) REVERT: 1 639 MET cc_start: 0.8419 (tpp) cc_final: 0.7496 (ttp) REVERT: 1 795 MET cc_start: 0.8184 (tmm) cc_final: 0.7856 (ppp) REVERT: 1 890 MET cc_start: 0.8015 (mmm) cc_final: 0.7566 (mmm) REVERT: 1 892 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7530 (mt0) REVERT: 1 1021 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7029 (ppp) REVERT: 1 1036 LEU cc_start: 0.9075 (mp) cc_final: 0.8580 (tt) REVERT: 1 1082 ASP cc_start: 0.7884 (t0) cc_final: 0.7171 (t0) REVERT: B 128 ASN cc_start: 0.6049 (p0) cc_final: 0.5770 (p0) outliers start: 19 outliers final: 15 residues processed: 204 average time/residue: 0.1920 time to fit residues: 55.2166 Evaluate side-chains 209 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 PHE Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 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 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 650 LEU Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 1016 SER Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1066 CYS 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: 0.1980 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN ** 11048 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.136806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119821 restraints weight = 14464.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122884 restraints weight = 8701.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125004 restraints weight = 6028.800| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8566 Z= 0.222 Angle : 0.706 15.199 11585 Z= 0.346 Chirality : 0.041 0.145 1310 Planarity : 0.004 0.055 1473 Dihedral : 4.541 24.702 1184 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.97 % Allowed : 23.64 % 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: -0.07 (0.26), residues: 1080 helix: 0.63 (0.21), residues: 628 sheet: -0.10 (0.86), residues: 45 loop : -1.03 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 986 HIS 0.003 0.001 HIS 1 483 PHE 0.036 0.002 PHE 1 546 TYR 0.027 0.002 TYR 1 674 ARG 0.005 0.000 ARG 11106 ********************** 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 211 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 65 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7286 (mmt-90) REVERT: 1 519 ILE cc_start: 0.8421 (mm) cc_final: 0.8049 (mt) REVERT: 1 631 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6644 (ttm110) REVERT: 1 639 MET cc_start: 0.8352 (tpp) cc_final: 0.7396 (ttp) REVERT: 1 795 MET cc_start: 0.8196 (tmm) cc_final: 0.7861 (ppp) REVERT: 1 890 MET cc_start: 0.8009 (mmm) cc_final: 0.7559 (mmm) REVERT: 1 892 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7534 (mt0) REVERT: 1 1021 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6959 (ppp) outliers start: 17 outliers final: 14 residues processed: 203 average time/residue: 0.2271 time to fit residues: 65.3265 Evaluate side-chains 203 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 123 PHE Chi-restraints excluded: chain 1 residue 137 ASP 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 523 CYS Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 1016 SER Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1066 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN ** 1 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 974 GLN ** 11048 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 = 0.3696 r_free = 0.3696 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121113 restraints weight = 14574.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124226 restraints weight = 8792.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126360 restraints weight = 6104.403| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8566 Z= 0.212 Angle : 0.704 15.129 11585 Z= 0.345 Chirality : 0.041 0.145 1310 Planarity : 0.004 0.053 1473 Dihedral : 4.495 24.389 1184 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.09 % Allowed : 24.33 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1080 helix: 0.73 (0.21), residues: 620 sheet: -0.03 (0.85), residues: 45 loop : -0.94 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 986 HIS 0.003 0.001 HIS 1 935 PHE 0.039 0.002 PHE 1 546 TYR 0.013 0.001 TYR 1 961 ARG 0.005 0.000 ARG 1 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.33 seconds wall clock time: 51 minutes 59.46 seconds (3119.46 seconds total)