Starting phenix.real_space_refine on Fri Aug 22 23:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mz6_3583/08_2025/5mz6_3583.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mz6_3583/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/5mz6_3583/08_2025/5mz6_3583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mz6_3583/08_2025/5mz6_3583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5mz6_3583/08_2025/5mz6_3583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mz6_3583/08_2025/5mz6_3583.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 20, 'ARG:plan': 5, 'ASP:plan': 16, 'PHE:plan': 1, 'ASN:plan1': 1} 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, 'ASP:plan': 7, 'GLU:plan': 8, 'TRP:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 1.57, per 1000 atoms: 0.19 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: 0.53 Conformation dependent library (CDL) restraints added in 207.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.31 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: 1.16 Time building geometry restraints manager: 0.70 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: 0.490 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.750 ------------------------------------------------------------------------------- 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 8567 Z= 0.251 Angle : 1.046 14.517 11587 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG 1 84 TYR 0.038 0.002 TYR 1 733 PHE 0.038 0.003 PHE 1 484 TRP 0.023 0.003 TRP 1 230 HIS 0.012 0.002 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8566) covalent geometry : angle 1.04585 (11585) SS BOND : bond 0.00726 ( 1) SS BOND : angle 2.35820 ( 2) hydrogen bonds : bond 0.30071 ( 387) hydrogen bonds : angle 10.37551 ( 1137) *********************** 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 : 0.239 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: 0.0791 time to fit residues: 33.4692 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 1 713 GLN 1 818 GLN 1 913 GLN 1 935 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120405 restraints weight = 14404.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123588 restraints weight = 8376.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125774 restraints weight = 5639.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127199 restraints weight = 4184.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128431 restraints weight = 3352.521| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8567 Z= 0.149 Angle : 0.636 8.550 11587 Z= 0.329 Chirality : 0.041 0.153 1310 Planarity : 0.005 0.057 1473 Dihedral : 5.474 27.627 1184 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.36 % Allowed : 13.44 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.21), residues: 1080 helix: -2.18 (0.16), residues: 613 sheet: -2.01 (0.78), residues: 45 loop : -2.18 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 378 TYR 0.019 0.002 TYR 1 961 PHE 0.024 0.002 PHE 1 875 TRP 0.012 0.001 TRP 1 230 HIS 0.005 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8566) covalent geometry : angle 0.63643 (11585) SS BOND : bond 0.00244 ( 1) SS BOND : angle 0.92604 ( 2) hydrogen bonds : bond 0.03775 ( 387) hydrogen bonds : angle 5.26335 ( 1137) *********************** 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 294 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 SER cc_start: 0.9153 (t) cc_final: 0.8785 (p) REVERT: 1 60 LEU cc_start: 0.9138 (tt) cc_final: 0.8850 (tp) REVERT: 1 65 ARG cc_start: 0.7377 (mtt180) cc_final: 0.7016 (mmt180) REVERT: 1 203 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8318 (mmtp) REVERT: 1 314 MET cc_start: 0.8868 (mmm) cc_final: 0.8626 (mmm) REVERT: 1 320 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8514 (tt) REVERT: 1 515 ILE cc_start: 0.8607 (mp) cc_final: 0.8197 (mt) REVERT: 1 519 ILE cc_start: 0.8763 (mm) cc_final: 0.7873 (mp) REVERT: 1 559 ARG cc_start: 0.8855 (ttt-90) cc_final: 0.8203 (ttt-90) REVERT: 1 573 GLN cc_start: 0.8836 (tt0) cc_final: 0.8595 (tt0) REVERT: 1 576 PHE cc_start: 0.7972 (m-10) cc_final: 0.7545 (m-10) REVERT: 1 652 ARG cc_start: 0.8140 (tmm160) cc_final: 0.7854 (ppt170) REVERT: 1 736 LYS cc_start: 0.9057 (tttt) cc_final: 0.8824 (ttmm) REVERT: 1 751 TYR cc_start: 0.8084 (t80) cc_final: 0.7832 (t80) REVERT: 1 846 MET cc_start: 0.8625 (mmm) cc_final: 0.8131 (mmp) REVERT: 1 890 MET cc_start: 0.8046 (mmm) cc_final: 0.7778 (mmm) REVERT: 1 1036 LEU cc_start: 0.8940 (mp) cc_final: 0.8634 (tt) REVERT: 1 1112 MET cc_start: 0.8264 (mtt) cc_final: 0.8028 (mtt) outliers start: 29 outliers final: 16 residues processed: 283 average time/residue: 0.0998 time to fit residues: 38.8449 Evaluate side-chains 233 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL 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 710 THR 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 941 LEU Chi-restraints excluded: chain 1 residue 955 ILE Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 483 HIS 1 485 ASN ** 1 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 644 ASN 1 713 GLN 1 910 HIS 1 935 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120227 restraints weight = 14250.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123407 restraints weight = 8169.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125661 restraints weight = 5453.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127223 restraints weight = 3976.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128149 restraints weight = 3142.659| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8567 Z= 0.134 Angle : 0.631 10.705 11587 Z= 0.317 Chirality : 0.041 0.135 1310 Planarity : 0.005 0.066 1473 Dihedral : 5.022 27.212 1184 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.71 % Allowed : 16.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.24), residues: 1080 helix: -0.90 (0.19), residues: 613 sheet: -0.87 (0.84), residues: 45 loop : -1.84 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 640 TYR 0.018 0.001 TYR 1 138 PHE 0.019 0.002 PHE 1 875 TRP 0.013 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8566) covalent geometry : angle 0.63089 (11585) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.40013 ( 2) hydrogen bonds : bond 0.03382 ( 387) hydrogen bonds : angle 4.74404 ( 1137) *********************** 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 265 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 SER cc_start: 0.8937 (t) cc_final: 0.8597 (p) REVERT: 1 58 ASN cc_start: 0.7971 (m110) cc_final: 0.7524 (t0) REVERT: 1 60 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8699 (tp) REVERT: 1 65 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7205 (mmt180) REVERT: 1 156 MET cc_start: 0.7995 (tpt) cc_final: 0.7735 (tpt) REVERT: 1 188 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6385 (tpt) REVERT: 1 465 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8274 (mm-30) REVERT: 1 519 ILE cc_start: 0.8573 (mm) cc_final: 0.7982 (mt) REVERT: 1 559 ARG cc_start: 0.8799 (ttt-90) cc_final: 0.8151 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8951 (tp40) cc_final: 0.8726 (tp40) REVERT: 1 570 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8671 (mp) REVERT: 1 573 GLN cc_start: 0.8777 (tt0) cc_final: 0.8491 (tt0) REVERT: 1 751 TYR cc_start: 0.8033 (t80) cc_final: 0.7818 (t80) REVERT: 1 846 MET cc_start: 0.8442 (mmm) cc_final: 0.7608 (mmm) REVERT: 1 890 MET cc_start: 0.8015 (mmm) cc_final: 0.7653 (mmm) REVERT: 1 1021 MET cc_start: 0.7985 (ppp) cc_final: 0.7625 (ppp) REVERT: 1 1036 LEU cc_start: 0.8850 (mp) cc_final: 0.8459 (tt) REVERT: 1 1112 MET cc_start: 0.8295 (mtt) cc_final: 0.7962 (mtp) REVERT: 1 1131 MET cc_start: 0.6925 (ptm) cc_final: 0.6392 (ttp) outliers start: 32 outliers final: 15 residues processed: 248 average time/residue: 0.0986 time to fit residues: 33.3979 Evaluate side-chains 227 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 60 LEU Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 188 MET Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 320 LEU Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 458 LEU Chi-restraints excluded: chain 1 residue 469 SER Chi-restraints excluded: chain 1 residue 570 LEU 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 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 40 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS 1 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119692 restraints weight = 14337.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122916 restraints weight = 8271.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125102 restraints weight = 5522.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126608 restraints weight = 4088.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127721 restraints weight = 3257.704| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8567 Z= 0.129 Angle : 0.605 9.023 11587 Z= 0.304 Chirality : 0.040 0.164 1310 Planarity : 0.004 0.066 1473 Dihedral : 4.792 26.339 1184 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.59 % Allowed : 17.73 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.25), residues: 1080 helix: -0.15 (0.20), residues: 617 sheet: -0.41 (0.87), residues: 45 loop : -1.66 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 1 490 TYR 0.016 0.001 TYR 1 138 PHE 0.027 0.002 PHE 1 576 TRP 0.014 0.001 TRP 1 288 HIS 0.012 0.001 HIS 1 483 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8566) covalent geometry : angle 0.60461 (11585) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.42690 ( 2) hydrogen bonds : bond 0.03109 ( 387) hydrogen bonds : angle 4.47550 ( 1137) *********************** 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 248 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 58 ASN cc_start: 0.7899 (m110) cc_final: 0.7479 (t0) REVERT: 1 65 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7226 (mmt180) REVERT: 1 156 MET cc_start: 0.7965 (tpt) cc_final: 0.7522 (tpt) REVERT: 1 188 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6421 (tpt) REVERT: 1 467 MET cc_start: 0.7994 (mmm) cc_final: 0.7642 (mmm) REVERT: 1 519 ILE cc_start: 0.8669 (mm) cc_final: 0.8128 (mp) REVERT: 1 559 ARG cc_start: 0.8760 (ttt-90) cc_final: 0.8078 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8953 (tp40) cc_final: 0.8742 (tp40) REVERT: 1 570 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8645 (mp) REVERT: 1 573 GLN cc_start: 0.8796 (tt0) cc_final: 0.8564 (tt0) REVERT: 1 578 MET cc_start: 0.7714 (mmp) cc_final: 0.7504 (mmp) REVERT: 1 585 MET cc_start: 0.7457 (mmp) cc_final: 0.6290 (mmp) REVERT: 1 751 TYR cc_start: 0.7882 (t80) cc_final: 0.7572 (t80) REVERT: 1 758 MET cc_start: 0.8406 (mmm) cc_final: 0.8174 (mmp) REVERT: 1 846 MET cc_start: 0.8527 (mmm) cc_final: 0.7538 (mmm) REVERT: 1 890 MET cc_start: 0.8029 (mmm) cc_final: 0.7647 (mmm) REVERT: 1 892 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7429 (mt0) REVERT: 1 964 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6187 (mt) REVERT: 1 1036 LEU cc_start: 0.8963 (mp) cc_final: 0.8578 (tt) REVERT: 1 1131 MET cc_start: 0.7021 (ptm) cc_final: 0.6717 (ptp) REVERT: B 123 GLU cc_start: 0.6216 (tp30) cc_final: 0.5730 (tp30) outliers start: 31 outliers final: 18 residues processed: 232 average time/residue: 0.0778 time to fit residues: 25.4942 Evaluate side-chains 223 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 188 MET Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 320 LEU 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 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 517 ASN 1 713 GLN ** 1 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117413 restraints weight = 14395.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120567 restraints weight = 8424.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122772 restraints weight = 5702.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124275 restraints weight = 4238.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125273 restraints weight = 3390.947| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8567 Z= 0.153 Angle : 0.621 7.759 11587 Z= 0.314 Chirality : 0.041 0.169 1310 Planarity : 0.004 0.068 1473 Dihedral : 4.768 26.996 1184 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.71 % Allowed : 18.77 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.25), residues: 1080 helix: 0.11 (0.20), residues: 616 sheet: -0.32 (0.87), residues: 45 loop : -1.53 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 11106 TYR 0.025 0.002 TYR 1 674 PHE 0.024 0.002 PHE 1 576 TRP 0.013 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8566) covalent geometry : angle 0.62100 (11585) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.37705 ( 2) hydrogen bonds : bond 0.03219 ( 387) hydrogen bonds : angle 4.49615 ( 1137) *********************** 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 237 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 156 MET cc_start: 0.7936 (tpt) cc_final: 0.7632 (tpt) REVERT: 1 188 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6395 (tpt) REVERT: 1 519 ILE cc_start: 0.8882 (mm) cc_final: 0.8232 (mp) REVERT: 1 559 ARG cc_start: 0.8774 (ttt-90) cc_final: 0.8154 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8988 (tp40) cc_final: 0.8306 (tm-30) REVERT: 1 570 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8664 (mp) REVERT: 1 890 MET cc_start: 0.8062 (mmm) cc_final: 0.7689 (mmm) REVERT: 1 892 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7527 (mt0) REVERT: 1 964 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6138 (mt) REVERT: 1 1036 LEU cc_start: 0.8999 (mp) cc_final: 0.8570 (tt) outliers start: 32 outliers final: 20 residues processed: 218 average time/residue: 0.0767 time to fit residues: 23.6968 Evaluate side-chains 208 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 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 276 SER Chi-restraints excluded: chain 1 residue 302 VAL Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 449 VAL Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 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 964 LEU Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN 1 713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118201 restraints weight = 14281.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121290 restraints weight = 8275.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123418 restraints weight = 5541.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124984 restraints weight = 4101.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126011 restraints weight = 3230.399| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8567 Z= 0.150 Angle : 0.630 8.694 11587 Z= 0.316 Chirality : 0.041 0.177 1310 Planarity : 0.004 0.068 1473 Dihedral : 4.725 26.409 1184 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.94 % Allowed : 19.70 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.26), residues: 1080 helix: 0.28 (0.21), residues: 618 sheet: -0.02 (0.93), residues: 40 loop : -1.43 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 11106 TYR 0.017 0.001 TYR 1 961 PHE 0.026 0.002 PHE 1 576 TRP 0.017 0.002 TRP 1 288 HIS 0.005 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8566) covalent geometry : angle 0.63027 (11585) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.32041 ( 2) hydrogen bonds : bond 0.03131 ( 387) hydrogen bonds : angle 4.45521 ( 1137) *********************** 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 227 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: 1 156 MET cc_start: 0.7933 (tpt) cc_final: 0.7584 (tpt) REVERT: 1 188 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6358 (tpt) REVERT: 1 388 ASN cc_start: 0.6326 (OUTLIER) cc_final: 0.5961 (p0) REVERT: 1 466 TYR cc_start: 0.8101 (t80) cc_final: 0.7553 (t80) REVERT: 1 519 ILE cc_start: 0.8702 (mm) cc_final: 0.8142 (mp) REVERT: 1 559 ARG cc_start: 0.8752 (ttt-90) cc_final: 0.8083 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8954 (tp40) cc_final: 0.8132 (tm-30) REVERT: 1 570 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8725 (mp) REVERT: 1 585 MET cc_start: 0.7625 (mmp) cc_final: 0.6886 (mmp) REVERT: 1 795 MET cc_start: 0.8183 (tmm) cc_final: 0.7920 (tmm) REVERT: 1 865 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: 1 890 MET cc_start: 0.8073 (mmm) cc_final: 0.7712 (mmm) REVERT: 1 892 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7007 (mt0) REVERT: 1 964 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5694 (mt) REVERT: 1 1036 LEU cc_start: 0.8996 (mp) cc_final: 0.8582 (tt) outliers start: 34 outliers final: 20 residues processed: 208 average time/residue: 0.0636 time to fit residues: 18.9164 Evaluate side-chains 208 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 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 276 SER Chi-restraints excluded: chain 1 residue 302 VAL Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118170 restraints weight = 14376.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121303 restraints weight = 8496.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123511 restraints weight = 5771.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124954 restraints weight = 4299.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126109 restraints weight = 3472.295| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8567 Z= 0.124 Angle : 0.619 8.731 11587 Z= 0.307 Chirality : 0.040 0.150 1310 Planarity : 0.004 0.065 1473 Dihedral : 4.552 27.016 1184 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.13 % Allowed : 21.67 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1080 helix: 0.57 (0.21), residues: 614 sheet: 0.09 (0.92), residues: 40 loop : -1.26 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 490 TYR 0.024 0.001 TYR 1 674 PHE 0.026 0.002 PHE 1 576 TRP 0.015 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8566) covalent geometry : angle 0.61935 (11585) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.22733 ( 2) hydrogen bonds : bond 0.02913 ( 387) hydrogen bonds : angle 4.29960 ( 1137) *********************** 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 231 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 58 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7434 (t0) REVERT: 1 156 MET cc_start: 0.7838 (tpt) cc_final: 0.7530 (tpt) REVERT: 1 465 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8172 (mm-30) REVERT: 1 466 TYR cc_start: 0.7764 (t80) cc_final: 0.7069 (t80) REVERT: 1 519 ILE cc_start: 0.8531 (mm) cc_final: 0.8044 (mt) REVERT: 1 569 GLN cc_start: 0.8918 (tp40) cc_final: 0.8696 (tp40) REVERT: 1 570 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8680 (mp) REVERT: 1 674 TYR cc_start: 0.7671 (t80) cc_final: 0.7397 (t80) REVERT: 1 685 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: 1 702 MET cc_start: 0.6158 (mmp) cc_final: 0.5933 (mmm) REVERT: 1 865 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8094 (m-10) REVERT: 1 890 MET cc_start: 0.7995 (mmm) cc_final: 0.7625 (mmm) REVERT: 1 892 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7049 (mt0) REVERT: 1 922 PHE cc_start: 0.8624 (m-80) cc_final: 0.8417 (m-80) REVERT: 1 964 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5676 (mt) REVERT: 1 1021 MET cc_start: 0.8606 (ppp) cc_final: 0.7652 (ppp) REVERT: 1 1036 LEU cc_start: 0.8916 (mp) cc_final: 0.8595 (tt) outliers start: 27 outliers final: 16 residues processed: 216 average time/residue: 0.0760 time to fit residues: 23.4993 Evaluate side-chains 205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 302 VAL Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117222 restraints weight = 14416.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120359 restraints weight = 8605.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122491 restraints weight = 5857.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124066 restraints weight = 4375.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125098 restraints weight = 3488.051| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8567 Z= 0.147 Angle : 0.648 10.195 11587 Z= 0.324 Chirality : 0.041 0.195 1310 Planarity : 0.004 0.060 1473 Dihedral : 4.582 25.535 1184 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.48 % Allowed : 21.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.26), residues: 1080 helix: 0.62 (0.21), residues: 612 sheet: 0.11 (0.90), residues: 40 loop : -1.32 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 130 TYR 0.022 0.001 TYR 1 674 PHE 0.029 0.002 PHE 1 576 TRP 0.015 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8566) covalent geometry : angle 0.64777 (11585) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.25187 ( 2) hydrogen bonds : bond 0.03064 ( 387) hydrogen bonds : angle 4.38486 ( 1137) *********************** 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 223 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 58 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7543 (t0) REVERT: 1 465 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8122 (mm-30) REVERT: 1 466 TYR cc_start: 0.8188 (t80) cc_final: 0.7753 (t80) REVERT: 1 519 ILE cc_start: 0.8816 (mm) cc_final: 0.8412 (mt) REVERT: 1 559 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8434 (ttt-90) REVERT: 1 569 GLN cc_start: 0.8855 (tp40) cc_final: 0.7974 (tm-30) REVERT: 1 570 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8663 (mp) REVERT: 1 685 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7462 (mtm-85) REVERT: 1 702 MET cc_start: 0.6542 (mmp) cc_final: 0.6333 (mmm) REVERT: 1 751 TYR cc_start: 0.8094 (t80) cc_final: 0.7873 (t80) REVERT: 1 795 MET cc_start: 0.8122 (tmm) cc_final: 0.7845 (ppp) REVERT: 1 865 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: 1 890 MET cc_start: 0.8026 (mmm) cc_final: 0.7635 (mmm) REVERT: 1 892 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7044 (mt0) REVERT: 1 964 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5823 (mt) REVERT: 1 1021 MET cc_start: 0.8606 (ppp) cc_final: 0.7733 (ppp) outliers start: 30 outliers final: 20 residues processed: 207 average time/residue: 0.0826 time to fit residues: 24.2492 Evaluate side-chains 210 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 302 VAL Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1137 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS ** 1 353 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 = 0.3617 r_free = 0.3617 target = 0.132440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115680 restraints weight = 14625.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118753 restraints weight = 8776.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120889 restraints weight = 6043.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122407 restraints weight = 4562.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123543 restraints weight = 3663.188| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8567 Z= 0.162 Angle : 0.671 11.817 11587 Z= 0.336 Chirality : 0.042 0.174 1310 Planarity : 0.004 0.059 1473 Dihedral : 4.706 25.507 1184 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.13 % Allowed : 22.83 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.26), residues: 1080 helix: 0.62 (0.21), residues: 608 sheet: 0.09 (0.89), residues: 40 loop : -1.30 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 130 TYR 0.020 0.002 TYR 1 138 PHE 0.038 0.002 PHE 11084 TRP 0.016 0.002 TRP 1 154 HIS 0.004 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8566) covalent geometry : angle 0.67139 (11585) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.25595 ( 2) hydrogen bonds : bond 0.03181 ( 387) hydrogen bonds : angle 4.49173 ( 1137) *********************** 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 223 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 58 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7512 (t0) REVERT: 1 465 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8112 (mm-30) REVERT: 1 466 TYR cc_start: 0.8018 (t80) cc_final: 0.7363 (t80) REVERT: 1 519 ILE cc_start: 0.8741 (mm) cc_final: 0.8300 (mt) REVERT: 1 569 GLN cc_start: 0.8852 (tp40) cc_final: 0.8250 (tm-30) REVERT: 1 570 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8689 (mp) REVERT: 1 751 TYR cc_start: 0.8136 (t80) cc_final: 0.7920 (t80) REVERT: 1 795 MET cc_start: 0.8163 (tmm) cc_final: 0.7868 (ppp) REVERT: 1 865 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8180 (m-10) REVERT: 1 890 MET cc_start: 0.8031 (mmm) cc_final: 0.7636 (mmm) REVERT: 1 892 GLN cc_start: 0.7721 (mm-40) cc_final: 0.6980 (mt0) REVERT: 1 964 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5911 (mt) REVERT: 1 1084 PHE cc_start: 0.8023 (t80) cc_final: 0.7809 (t80) outliers start: 27 outliers final: 20 residues processed: 209 average time/residue: 0.0901 time to fit residues: 26.5112 Evaluate side-chains 211 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 302 VAL Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1137 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS 1 517 ASN ** 1 689 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 = 0.3631 r_free = 0.3631 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116779 restraints weight = 14453.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119924 restraints weight = 8578.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122125 restraints weight = 5834.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123587 restraints weight = 4352.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124796 restraints weight = 3492.555| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8567 Z= 0.144 Angle : 0.669 13.168 11587 Z= 0.334 Chirality : 0.041 0.160 1310 Planarity : 0.004 0.057 1473 Dihedral : 4.634 25.003 1184 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.01 % Allowed : 22.48 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 1080 helix: 0.65 (0.21), residues: 614 sheet: 0.08 (0.88), residues: 40 loop : -1.30 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 1 707 TYR 0.025 0.002 TYR 1 674 PHE 0.048 0.002 PHE 11084 TRP 0.014 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 935 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8566) covalent geometry : angle 0.66876 (11585) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.25830 ( 2) hydrogen bonds : bond 0.03122 ( 387) hydrogen bonds : angle 4.49850 ( 1137) ********************** 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 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 58 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7497 (t0) REVERT: 1 465 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8103 (mm-30) REVERT: 1 466 TYR cc_start: 0.7976 (t80) cc_final: 0.7276 (t80) REVERT: 1 519 ILE cc_start: 0.8715 (mm) cc_final: 0.8310 (mt) REVERT: 1 569 GLN cc_start: 0.8913 (tp40) cc_final: 0.8222 (tm-30) REVERT: 1 751 TYR cc_start: 0.8148 (t80) cc_final: 0.7930 (t80) REVERT: 1 795 MET cc_start: 0.8145 (tmm) cc_final: 0.7832 (ppp) REVERT: 1 865 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: 1 890 MET cc_start: 0.7992 (mmm) cc_final: 0.7591 (mmm) REVERT: 1 892 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7492 (mt0) REVERT: 1 964 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5703 (mt) outliers start: 26 outliers final: 19 residues processed: 202 average time/residue: 0.0833 time to fit residues: 24.4126 Evaluate side-chains 212 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 58 ASN Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 941 LEU Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1108 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS ** 1 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 689 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 = 0.3631 r_free = 0.3631 target = 0.133386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116679 restraints weight = 14413.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119776 restraints weight = 8702.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121943 restraints weight = 5998.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123546 restraints weight = 4508.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124516 restraints weight = 3593.888| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8567 Z= 0.155 Angle : 0.704 13.415 11587 Z= 0.349 Chirality : 0.041 0.151 1310 Planarity : 0.004 0.057 1473 Dihedral : 4.648 25.110 1184 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.78 % Allowed : 22.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.26), residues: 1080 helix: 0.63 (0.21), residues: 615 sheet: -0.49 (0.76), residues: 51 loop : -1.26 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 130 TYR 0.021 0.002 TYR 1 138 PHE 0.025 0.002 PHE 11084 TRP 0.014 0.001 TRP 1 154 HIS 0.003 0.001 HIS 1 738 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8566) covalent geometry : angle 0.70416 (11585) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.21754 ( 2) hydrogen bonds : bond 0.03271 ( 387) hydrogen bonds : angle 4.55625 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.24 seconds wall clock time: 23 minutes 30.48 seconds (1410.48 seconds total)