Starting phenix.real_space_refine on Sun May 18 11:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4y_14510/05_2025/7z4y_14510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4y_14510/05_2025/7z4y_14510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4y_14510/05_2025/7z4y_14510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4y_14510/05_2025/7z4y_14510.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4y_14510/05_2025/7z4y_14510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4y_14510/05_2025/7z4y_14510.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 102 5.16 5 C 10676 2.51 5 N 2863 2.21 5 O 3115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16756 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1184 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7198 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 40, 'TRANS': 887} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1208 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 14, 'ARG:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7166 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 888} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 10.33, per 1000 atoms: 0.62 Number of scatterers: 16756 At special positions: 0 Unit cell: (99.554, 120.34, 233.022, 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 102 16.00 O 3115 8.00 N 2863 7.00 C 10676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 9 sheets defined 47.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 43 through 74 removed outlier: 4.060A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.756A pdb=" N ILE A 112 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.622A pdb=" N TYR B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.982A pdb=" N SER B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.627A pdb=" N GLU B 245 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 264 through 273 removed outlier: 4.141A pdb=" N GLU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.255A pdb=" N PHE B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.727A pdb=" N PHE B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.642A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG B 384 " --> pdb=" O MET B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.682A pdb=" N GLU B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.601A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Proline residue: B 446 - end of helix removed outlier: 3.735A pdb=" N ARG B 450 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 474 removed outlier: 4.646A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 466 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 removed outlier: 3.687A pdb=" N ALA B 486 " --> pdb=" O GLU B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.575A pdb=" N VAL B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 removed outlier: 4.131A pdb=" N GLU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 597 through 615 WARNING: missing atoms! Processing helix chain 'B' and resid 620 through 645 removed outlier: 4.002A pdb=" N VAL B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 703 through 710 removed outlier: 3.849A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 767 Processing helix chain 'B' and resid 789 through 806 Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.303A pdb=" N ASN B 811 " --> pdb=" O HIS B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 840 Processing helix chain 'B' and resid 848 through 862 removed outlier: 3.744A pdb=" N LEU B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 860 " --> pdb=" O ARG B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 879 removed outlier: 4.179A pdb=" N ALA B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 879 " --> pdb=" O ARG B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 894 removed outlier: 3.988A pdb=" N LEU B 888 " --> pdb=" O ASP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 910 removed outlier: 4.246A pdb=" N ALA B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 908 " --> pdb=" O GLN B 904 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 910 " --> pdb=" O THR B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 925 through 948 Proline residue: B 931 - end of helix removed outlier: 3.539A pdb=" N CYS B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 962 removed outlier: 4.242A pdb=" N PHE B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 974 Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.678A pdb=" N CYS B 996 " --> pdb=" O SER B 992 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1000 " --> pdb=" O CYS B 996 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS B1012 " --> pdb=" O CYS B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1029 removed outlier: 3.531A pdb=" N LYS B1029 " --> pdb=" O GLU B1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 74 removed outlier: 5.091A pdb=" N LYS C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.911A pdb=" N GLN C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 126 removed outlier: 4.219A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 3.937A pdb=" N ASN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.797A pdb=" N GLY D 166 " --> pdb=" O THR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 181 removed outlier: 4.206A pdb=" N ALA D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.669A pdb=" N GLU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 removed outlier: 4.140A pdb=" N MET D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.501A pdb=" N MET D 257 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 273 removed outlier: 3.576A pdb=" N THR D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE D 270 " --> pdb=" O TRP D 266 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 300 removed outlier: 4.166A pdb=" N PHE D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 353 removed outlier: 4.217A pdb=" N PHE D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.756A pdb=" N ARG D 384 " --> pdb=" O MET D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 413 through 430 removed outlier: 3.548A pdb=" N GLU D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN D 426 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 427 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 removed outlier: 4.056A pdb=" N ASP D 435 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 451 Proline residue: D 446 - end of helix removed outlier: 3.611A pdb=" N ARG D 450 " --> pdb=" O PRO D 446 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 451 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 474 removed outlier: 3.550A pdb=" N GLU D 473 " --> pdb=" O ILE D 469 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 522 removed outlier: 4.391A pdb=" N GLN D 519 " --> pdb=" O GLY D 515 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET D 520 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 580 through 587 removed outlier: 3.528A pdb=" N MET D 584 " --> pdb=" O ASN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 Processing helix chain 'D' and resid 597 through 616 WARNING: missing atoms! removed outlier: 3.803A pdb=" N ILE D 615 " --> pdb=" O GLN D 611 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 616 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 641 removed outlier: 4.080A pdb=" N GLU D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 654 Processing helix chain 'D' and resid 703 through 709 removed outlier: 4.153A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 736 No H-bonds generated for 'chain 'D' and resid 734 through 736' Processing helix chain 'D' and resid 755 through 770 removed outlier: 4.229A pdb=" N VAL D 759 " --> pdb=" O ASN D 755 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 768 " --> pdb=" O GLN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 805 Processing helix chain 'D' and resid 814 through 845 removed outlier: 3.955A pdb=" N VAL D 818 " --> pdb=" O ASN D 814 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 842 " --> pdb=" O GLU D 838 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG D 843 " --> pdb=" O LEU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 862 Processing helix chain 'D' and resid 871 through 878 removed outlier: 4.180A pdb=" N ALA D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS D 878 " --> pdb=" O GLY D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 895 removed outlier: 3.624A pdb=" N LEU D 888 " --> pdb=" O ASP D 884 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 890 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 891 " --> pdb=" O LEU D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 907 removed outlier: 3.707A pdb=" N ALA D 907 " --> pdb=" O GLU D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 913 Processing helix chain 'D' and resid 925 through 948 Proline residue: D 931 - end of helix removed outlier: 3.561A pdb=" N GLN D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 945 " --> pdb=" O ARG D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 962 removed outlier: 3.522A pdb=" N SER D 960 " --> pdb=" O GLU D 956 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE D 962 " --> pdb=" O TYR D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 974 Processing helix chain 'D' and resid 978 through 983 Processing helix chain 'D' and resid 989 through 1012 removed outlier: 3.779A pdb=" N ILE D 993 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS D 996 " --> pdb=" O SER D 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG D 998 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D1003 " --> pdb=" O ARG D 999 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D1005 " --> pdb=" O GLU D1001 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN D1006 " --> pdb=" O GLU D1002 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS D1012 " --> pdb=" O CYS D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1029 removed outlier: 3.730A pdb=" N LYS D1029 " --> pdb=" O GLU D1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.773A pdb=" N VAL A 172 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 97 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A 174 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU C 95 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.001A pdb=" N SER B 156 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE B 307 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 158 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 157 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER B 283 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 159 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 186 " --> pdb=" O TRP B 248 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 250 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY B 210 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 329 through 330 removed outlier: 3.587A pdb=" N VAL B 539 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 496 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N MET B 538 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE B 498 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 389 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA B 481 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 391 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 502 through 504 Processing sheet with id=AA5, first strand: chain 'B' and resid 725 through 732 removed outlier: 5.975A pdb=" N LEU B 699 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 674 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ARG B 701 " --> pdb=" O GLY B 672 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N GLY B 672 " --> pdb=" O ARG B 701 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 738 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 99 through 101 removed outlier: 6.967A pdb=" N SER D 156 " --> pdb=" O HIS D 305 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE D 307 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 158 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 157 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG D 184 " --> pdb=" O TRP D 248 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ILE D 250 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE D 186 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL D 185 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET D 227 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE D 187 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 316 through 322 removed outlier: 3.515A pdb=" N VAL D 539 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 538 " --> pdb=" O PHE D 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 502 through 504 Processing sheet with id=AA9, first strand: chain 'D' and resid 727 through 732 removed outlier: 3.796A pdb=" N VAL D 673 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP D 668 " --> pdb=" O ASN D 664 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASN D 664 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY D 670 " --> pdb=" O VAL D 662 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 662 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG D 658 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU D 659 " --> pdb=" O SER D 740 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1995 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: 5.52 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3651 1.33 - 1.45: 3485 1.45 - 1.57: 9772 1.57 - 1.69: 0 1.69 - 1.81: 166 Bond restraints: 17074 Sorted by residual: bond pdb=" N VAL D 845 " pdb=" CA VAL D 845 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.12e-02 7.97e+03 1.82e+01 bond pdb=" C THR D 844 " pdb=" N VAL D 845 " ideal model delta sigma weight residual 1.332 1.350 -0.018 5.60e-03 3.19e+04 1.03e+01 bond pdb=" N LYS D 841 " pdb=" CA LYS D 841 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.16e-02 7.43e+03 8.49e+00 bond pdb=" N ILE B 547 " pdb=" CA ILE B 547 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.21e-02 6.83e+03 7.94e+00 bond pdb=" N VAL B 845 " pdb=" CA VAL B 845 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.94e+00 ... (remaining 17069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 22489 2.02 - 4.04: 575 4.04 - 6.06: 64 6.06 - 8.07: 23 8.07 - 10.09: 4 Bond angle restraints: 23155 Sorted by residual: angle pdb=" C VAL D 845 " pdb=" CA VAL D 845 " pdb=" CB VAL D 845 " ideal model delta sigma weight residual 111.74 106.47 5.27 9.40e-01 1.13e+00 3.14e+01 angle pdb=" C VAL D 845 " pdb=" N LEU D 846 " pdb=" CA LEU D 846 " ideal model delta sigma weight residual 121.76 129.80 -8.04 1.51e+00 4.39e-01 2.84e+01 angle pdb=" N GLU B 765 " pdb=" CA GLU B 765 " pdb=" CB GLU B 765 " ideal model delta sigma weight residual 110.28 117.29 -7.01 1.55e+00 4.16e-01 2.04e+01 angle pdb=" N GLU B 201 " pdb=" CA GLU B 201 " pdb=" CB GLU B 201 " ideal model delta sigma weight residual 110.01 116.25 -6.24 1.45e+00 4.76e-01 1.85e+01 angle pdb=" N LYS D 182 " pdb=" CA LYS D 182 " pdb=" C LYS D 182 " ideal model delta sigma weight residual 111.28 116.61 -5.33 1.35e+00 5.49e-01 1.56e+01 ... (remaining 23150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9418 17.85 - 35.70: 801 35.70 - 53.56: 141 53.56 - 71.41: 29 71.41 - 89.26: 16 Dihedral angle restraints: 10405 sinusoidal: 3972 harmonic: 6433 Sorted by residual: dihedral pdb=" CA HIS D 300 " pdb=" C HIS D 300 " pdb=" N LYS D 301 " pdb=" CA LYS D 301 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN D1006 " pdb=" C GLN D1006 " pdb=" N MET D1007 " pdb=" CA MET D1007 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG C 79 " pdb=" C ARG C 79 " pdb=" N PRO C 80 " pdb=" CA PRO C 80 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 10402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2574 0.111 - 0.221: 89 0.221 - 0.331: 5 0.331 - 0.442: 0 0.442 - 0.552: 1 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CB VAL D 845 " pdb=" CA VAL D 845 " pdb=" CG1 VAL D 845 " pdb=" CG2 VAL D 845 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA ARG B 751 " pdb=" N ARG B 751 " pdb=" C ARG B 751 " pdb=" CB ARG B 751 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE B 547 " pdb=" N ILE B 547 " pdb=" C ILE B 547 " pdb=" CB ILE B 547 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2666 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 778 " 0.061 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO B 779 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 779 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 779 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 126 " -0.060 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO B 127 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 118 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C ASN A 118 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 118 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 119 " 0.016 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 533 2.70 - 3.25: 17764 3.25 - 3.80: 25897 3.80 - 4.35: 32819 4.35 - 4.90: 52006 Nonbonded interactions: 129019 Sorted by model distance: nonbonded pdb=" OD1 ASN B 676 " pdb=" N PHE B 677 " model vdw 2.154 3.120 nonbonded pdb=" O PRO D 808 " pdb=" O LEU D 809 " model vdw 2.163 3.040 nonbonded pdb=" O HIS B 802 " pdb=" OG SER B 806 " model vdw 2.205 3.040 nonbonded pdb=" O LEU D 404 " pdb=" OG1 THR D 407 " model vdw 2.218 3.040 nonbonded pdb=" O THR D 972 " pdb=" OG1 THR D 975 " model vdw 2.227 3.040 ... (remaining 129014 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 89 or (resid 90 through 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 100 or (re \ sid 101 through 103 and (name N or name CA or name C or name O or name CB )) or \ resid 104 through 120 or (resid 121 and (name N or name CA or name C or name O o \ r name CB )) or resid 122 through 123 or (resid 124 through 125 and (name N or n \ ame CA or name C or name O or name CB )) or resid 126 through 131 or (resid 132 \ through 136 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 7 through 148 or (resid 149 through 165 and (name N or name CA or name C or name \ O or name CB )) or resid 166 through 195 or (resid 196 and (name N or name CA o \ r name C or name O or name CB )) or resid 197 through 198 or (resid 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 218)) selection = (chain 'C' and ((resid 43 through 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 84 or (resid 85 through 91 and (n \ ame N or name CA or name C or name O or name CB )) or resid 92 through 130 or (r \ esid 131 through 136 and (name N or name CA or name C or name O or name CB )) or \ resid 137 through 147 or (resid 148 through 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 211 or (resid 212 \ through 214 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 15 through 218)) } ncs_group { reference = (chain 'B' and (resid 96 through 619 or (resid 620 through 621 and (name N or na \ me CA or name C or name O or name CB )) or resid 622 through 637 or (resid 638 t \ hrough 639 and (name N or name CA or name C or name O or name CB )) or resid 640 \ through 703 or (resid 704 and (name N or name CA or name C or name O or name CB \ )) or resid 705 through 724 or (resid 725 through 726 and (name N or name CA or \ name C or name O or name CB )) or resid 727 through 744 or (resid 745 and (name \ N or name CA or name C or name O or name CB )) or resid 746 through 773 or (res \ id 774 and (name N or name CA or name C or name O or name CB )) or resid 775 thr \ ough 792 or (resid 793 through 794 and (name N or name CA or name C or name O or \ name CB )) or resid 795 or (resid 796 through 801 and (name N or name CA or nam \ e C or name O or name CB )) or resid 802 or (resid 803 through 805 and (name N o \ r name CA or name C or name O or name CB )) or resid 806 through 1042)) selection = (chain 'D' and (resid 96 through 629 or (resid 630 through 636 and (name N or na \ me CA or name C or name O or name CB )) or resid 637 through 641 or (resid 642 a \ nd (name N or name CA or name C or name O or name CB )) or resid 643 through 663 \ or (resid 664 through 665 and (name N or name CA or name C or name O or name CB \ )) or resid 666 or (resid 667 and (name N or name CA or name C or name O or nam \ e CB )) or resid 668 through 677 or (resid 678 through 684 and (name N or name C \ A or name C or name O or name CB )) or resid 685 through 718 or (resid 719 and ( \ name N or name CA or name C or name O or name CB )) or resid 720 or (resid 721 t \ hrough 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ through 730 or (resid 731 and (name N or name CA or name C or name O or name CB \ )) or resid 732 through 763 or (resid 764 and (name N or name CA or name C or n \ ame O or name CB )) or resid 765 through 779 or (resid 780 and (name N or name C \ A or name C or name O or name CB )) or resid 781 through 1042)) } 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=0.00 max=1.00 mean=0.99 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: 3.810 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.450 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.003 0.059 17074 Z= 0.193 Angle : 0.741 10.093 23155 Z= 0.416 Chirality : 0.050 0.552 2669 Planarity : 0.005 0.093 3004 Dihedral : 14.192 89.259 6223 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.60 % Allowed : 1.88 % Favored : 97.52 % Rotamer: Outliers : 0.46 % Allowed : 0.58 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2181 helix: 0.04 (0.17), residues: 895 sheet: 0.39 (0.39), residues: 170 loop : -2.89 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 266 HIS 0.007 0.001 HIS B 318 PHE 0.023 0.002 PHE A 115 TYR 0.028 0.001 TYR A 108 ARG 0.006 0.000 ARG B 933 Details of bonding type rmsd hydrogen bonds : bond 0.20147 ( 696) hydrogen bonds : angle 6.67388 ( 1995) covalent geometry : bond 0.00331 (17074) covalent geometry : angle 0.74051 (23155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 436 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.8288 (m110) cc_final: 0.7965 (m-40) REVERT: B 140 LEU cc_start: 0.8880 (mm) cc_final: 0.8551 (mm) REVERT: B 146 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8568 (mt-10) REVERT: B 257 MET cc_start: 0.7481 (mmm) cc_final: 0.5736 (mmm) REVERT: B 279 TYR cc_start: 0.8480 (m-80) cc_final: 0.8162 (m-80) REVERT: B 347 MET cc_start: 0.8997 (ptp) cc_final: 0.8550 (mtm) REVERT: B 390 ILE cc_start: 0.9542 (tp) cc_final: 0.9338 (tp) REVERT: B 456 HIS cc_start: 0.8256 (p90) cc_final: 0.7749 (p-80) REVERT: B 482 THR cc_start: 0.6658 (m) cc_final: 0.6360 (m) REVERT: B 495 THR cc_start: 0.8944 (t) cc_final: 0.8637 (m) REVERT: B 538 MET cc_start: 0.8538 (ppp) cc_final: 0.7804 (ppp) REVERT: B 650 CYS cc_start: 0.7930 (p) cc_final: 0.7646 (p) REVERT: B 750 LEU cc_start: 0.7007 (mp) cc_final: 0.6334 (tp) REVERT: B 809 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.5962 (mt) REVERT: C 74 LEU cc_start: 0.8443 (mt) cc_final: 0.8161 (mt) REVERT: C 100 MET cc_start: 0.8568 (mmm) cc_final: 0.8282 (mmm) REVERT: D 122 TYR cc_start: 0.8639 (p90) cc_final: 0.8315 (t80) REVERT: D 202 MET cc_start: 0.7902 (ptp) cc_final: 0.7346 (ptp) REVERT: D 203 TYR cc_start: 0.8334 (t80) cc_final: 0.7575 (t80) REVERT: D 212 MET cc_start: 0.1027 (tpt) cc_final: -0.1036 (mmt) REVERT: D 281 PHE cc_start: 0.7716 (m-10) cc_final: 0.7291 (m-10) REVERT: D 299 LEU cc_start: 0.8030 (mt) cc_final: 0.7432 (mt) REVERT: D 308 TYR cc_start: 0.7701 (t80) cc_final: 0.7427 (t80) REVERT: D 382 MET cc_start: 0.7822 (mmp) cc_final: 0.7603 (mmp) REVERT: D 487 MET cc_start: 0.4312 (tpt) cc_final: 0.4093 (tpt) REVERT: D 676 ASN cc_start: 0.8478 (t0) cc_final: 0.7907 (t0) REVERT: D 1031 LYS cc_start: 0.8574 (pttm) cc_final: 0.7998 (tptt) outliers start: 8 outliers final: 2 residues processed: 441 average time/residue: 0.2616 time to fit residues: 176.2969 Evaluate side-chains 372 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 369 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 171 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 HIS B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS D 300 HIS ** D 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 757 GLN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.133110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093126 restraints weight = 58849.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.095317 restraints weight = 40473.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096909 restraints weight = 30767.175| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17074 Z= 0.157 Angle : 0.634 8.250 23155 Z= 0.337 Chirality : 0.044 0.152 2669 Planarity : 0.005 0.063 3004 Dihedral : 4.819 21.329 2346 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.85 % Favored : 90.83 % Rotamer: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2181 helix: 0.56 (0.17), residues: 951 sheet: 0.48 (0.39), residues: 182 loop : -2.82 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 266 HIS 0.012 0.001 HIS C 209 PHE 0.017 0.001 PHE A 166 TYR 0.011 0.001 TYR D 819 ARG 0.009 0.001 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 696) hydrogen bonds : angle 4.78020 ( 1995) covalent geometry : bond 0.00339 (17074) covalent geometry : angle 0.63442 (23155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8574 (mmtm) REVERT: A 75 ASN cc_start: 0.9246 (m-40) cc_final: 0.8746 (m-40) REVERT: A 95 LEU cc_start: 0.9085 (mp) cc_final: 0.8826 (mp) REVERT: A 179 CYS cc_start: 0.7776 (m) cc_final: 0.7410 (m) REVERT: A 199 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 140 LEU cc_start: 0.8906 (mm) cc_final: 0.8509 (mm) REVERT: B 212 MET cc_start: 0.8303 (tpt) cc_final: 0.8083 (tpt) REVERT: B 253 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 257 MET cc_start: 0.7618 (mmm) cc_final: 0.6967 (mmt) REVERT: B 347 MET cc_start: 0.8863 (ptp) cc_final: 0.8577 (ptt) REVERT: B 402 TYR cc_start: 0.8994 (m-80) cc_final: 0.8755 (m-80) REVERT: B 406 MET cc_start: 0.8858 (mmp) cc_final: 0.8652 (mmp) REVERT: B 456 HIS cc_start: 0.8858 (p90) cc_final: 0.8142 (p-80) REVERT: B 538 MET cc_start: 0.8752 (ppp) cc_final: 0.8037 (ppp) REVERT: B 658 ARG cc_start: 0.7666 (mmp-170) cc_final: 0.7340 (mmp-170) REVERT: B 700 LEU cc_start: 0.9563 (mm) cc_final: 0.9250 (mm) REVERT: B 944 LYS cc_start: 0.9478 (mmtm) cc_final: 0.9267 (mmmt) REVERT: B 967 MET cc_start: 0.8406 (mpp) cc_final: 0.8016 (mpp) REVERT: B 979 PHE cc_start: 0.8937 (t80) cc_final: 0.8314 (t80) REVERT: B 1007 MET cc_start: 0.9394 (mmp) cc_final: 0.9135 (mmp) REVERT: C 181 ASP cc_start: 0.8538 (t0) cc_final: 0.8276 (t0) REVERT: C 185 GLN cc_start: 0.9056 (mp10) cc_final: 0.8851 (mp10) REVERT: D 122 TYR cc_start: 0.8590 (p90) cc_final: 0.8259 (t80) REVERT: D 212 MET cc_start: -0.0244 (tpt) cc_final: -0.1376 (mmt) REVERT: D 281 PHE cc_start: 0.8106 (m-10) cc_final: 0.7858 (m-10) REVERT: D 296 ILE cc_start: 0.9444 (mm) cc_final: 0.9219 (mm) REVERT: D 308 TYR cc_start: 0.7572 (t80) cc_final: 0.7284 (t80) REVERT: D 676 ASN cc_start: 0.8786 (t0) cc_final: 0.8480 (t0) REVERT: D 985 MET cc_start: 0.7939 (mpp) cc_final: 0.7272 (pmm) REVERT: D 1031 LYS cc_start: 0.8522 (pttm) cc_final: 0.7982 (tptt) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.2636 time to fit residues: 179.5093 Evaluate side-chains 365 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 47 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092533 restraints weight = 58458.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094863 restraints weight = 40352.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096382 restraints weight = 30623.281| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17074 Z= 0.135 Angle : 0.603 8.346 23155 Z= 0.320 Chirality : 0.043 0.160 2669 Planarity : 0.005 0.069 3004 Dihedral : 4.798 26.603 2346 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.89 % Favored : 91.88 % Rotamer: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2181 helix: 0.67 (0.17), residues: 950 sheet: 0.45 (0.39), residues: 182 loop : -2.72 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 511 HIS 0.008 0.001 HIS D 594 PHE 0.035 0.001 PHE B1023 TYR 0.013 0.001 TYR B 256 ARG 0.007 0.000 ARG B 933 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 696) hydrogen bonds : angle 4.38769 ( 1995) covalent geometry : bond 0.00296 (17074) covalent geometry : angle 0.60278 (23155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8520 (mmtm) REVERT: A 75 ASN cc_start: 0.9282 (m-40) cc_final: 0.8804 (m-40) REVERT: A 177 ASN cc_start: 0.9378 (t0) cc_final: 0.9139 (t0) REVERT: A 179 CYS cc_start: 0.7874 (m) cc_final: 0.7574 (m) REVERT: A 199 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7362 (tm-30) REVERT: B 140 LEU cc_start: 0.8912 (mm) cc_final: 0.8544 (mm) REVERT: B 251 PHE cc_start: 0.8510 (m-80) cc_final: 0.7483 (m-80) REVERT: B 257 MET cc_start: 0.7895 (mmm) cc_final: 0.7272 (mmt) REVERT: B 264 VAL cc_start: 0.8689 (t) cc_final: 0.8460 (t) REVERT: B 347 MET cc_start: 0.8878 (ptp) cc_final: 0.8586 (ptt) REVERT: B 406 MET cc_start: 0.8898 (mmp) cc_final: 0.8582 (mmm) REVERT: B 456 HIS cc_start: 0.8851 (p90) cc_final: 0.8174 (p-80) REVERT: B 460 LEU cc_start: 0.9448 (mt) cc_final: 0.9170 (mt) REVERT: B 485 PHE cc_start: 0.9106 (t80) cc_final: 0.8869 (t80) REVERT: B 538 MET cc_start: 0.8820 (ppp) cc_final: 0.8048 (ppp) REVERT: B 650 CYS cc_start: 0.7967 (p) cc_final: 0.7765 (p) REVERT: B 700 LEU cc_start: 0.9455 (mm) cc_final: 0.9162 (mm) REVERT: B 743 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: B 944 LYS cc_start: 0.9460 (mmtm) cc_final: 0.9240 (mmmt) REVERT: B 958 TYR cc_start: 0.9088 (t80) cc_final: 0.8830 (t80) REVERT: B 979 PHE cc_start: 0.8937 (t80) cc_final: 0.8381 (t80) REVERT: B 1007 MET cc_start: 0.9401 (mmp) cc_final: 0.9182 (mmp) REVERT: C 181 ASP cc_start: 0.8710 (t0) cc_final: 0.8480 (t0) REVERT: C 185 GLN cc_start: 0.9144 (mp10) cc_final: 0.8855 (mp10) REVERT: D 122 TYR cc_start: 0.8466 (p90) cc_final: 0.8132 (t80) REVERT: D 212 MET cc_start: -0.0389 (tpt) cc_final: -0.1616 (mmt) REVERT: D 281 PHE cc_start: 0.8097 (m-10) cc_final: 0.7873 (m-10) REVERT: D 308 TYR cc_start: 0.7530 (t80) cc_final: 0.7278 (t80) REVERT: D 676 ASN cc_start: 0.8858 (t0) cc_final: 0.8562 (t0) REVERT: D 994 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7442 (mt) REVERT: D 996 CYS cc_start: 0.8761 (p) cc_final: 0.8486 (p) REVERT: D 1030 ILE cc_start: 0.9174 (pt) cc_final: 0.8920 (pt) REVERT: D 1031 LYS cc_start: 0.8533 (pttm) cc_final: 0.8047 (tptt) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.2698 time to fit residues: 186.6759 Evaluate side-chains 373 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 160 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 211 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** D 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 GLN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.132071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091714 restraints weight = 58870.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094160 restraints weight = 39990.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095935 restraints weight = 30110.486| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17074 Z= 0.113 Angle : 0.583 7.746 23155 Z= 0.307 Chirality : 0.043 0.161 2669 Planarity : 0.004 0.074 3004 Dihedral : 4.614 22.227 2346 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.62 % Favored : 91.15 % Rotamer: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2181 helix: 0.76 (0.17), residues: 949 sheet: 0.24 (0.39), residues: 195 loop : -2.61 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 511 HIS 0.012 0.001 HIS A 109 PHE 0.016 0.001 PHE D 509 TYR 0.012 0.001 TYR B 256 ARG 0.005 0.000 ARG D 502 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 696) hydrogen bonds : angle 4.16164 ( 1995) covalent geometry : bond 0.00250 (17074) covalent geometry : angle 0.58331 (23155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.9454 (t0) cc_final: 0.9193 (t0) REVERT: A 199 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 140 LEU cc_start: 0.8915 (mm) cc_final: 0.8511 (mm) REVERT: B 251 PHE cc_start: 0.8617 (m-80) cc_final: 0.7644 (m-80) REVERT: B 347 MET cc_start: 0.8898 (ptp) cc_final: 0.8564 (ptt) REVERT: B 398 ASP cc_start: 0.8950 (m-30) cc_final: 0.8162 (m-30) REVERT: B 402 TYR cc_start: 0.8966 (m-80) cc_final: 0.8711 (m-80) REVERT: B 406 MET cc_start: 0.8935 (mmp) cc_final: 0.8629 (mmm) REVERT: B 456 HIS cc_start: 0.8890 (p90) cc_final: 0.8358 (p-80) REVERT: B 460 LEU cc_start: 0.9430 (mt) cc_final: 0.9175 (mt) REVERT: B 538 MET cc_start: 0.8894 (ppp) cc_final: 0.8090 (ppp) REVERT: B 560 ASN cc_start: 0.8605 (m110) cc_final: 0.8405 (m110) REVERT: B 944 LYS cc_start: 0.9420 (mmtm) cc_final: 0.9188 (mmmt) REVERT: B 999 ARG cc_start: 0.8921 (mpp-170) cc_final: 0.8611 (mpp-170) REVERT: B 1007 MET cc_start: 0.9324 (mmp) cc_final: 0.9072 (mmp) REVERT: C 71 LYS cc_start: 0.9530 (tmtt) cc_final: 0.9327 (tmtt) REVERT: C 136 PHE cc_start: 0.8768 (m-10) cc_final: 0.8349 (t80) REVERT: C 181 ASP cc_start: 0.8788 (t0) cc_final: 0.8505 (t0) REVERT: C 185 GLN cc_start: 0.9007 (mp10) cc_final: 0.8797 (mp10) REVERT: D 122 TYR cc_start: 0.8464 (p90) cc_final: 0.8127 (t80) REVERT: D 212 MET cc_start: -0.0316 (tpt) cc_final: -0.1492 (mmt) REVERT: D 281 PHE cc_start: 0.8141 (m-10) cc_final: 0.7839 (m-10) REVERT: D 308 TYR cc_start: 0.7558 (t80) cc_final: 0.7322 (t80) REVERT: D 310 ASP cc_start: 0.7665 (p0) cc_final: 0.7457 (p0) REVERT: D 676 ASN cc_start: 0.8803 (t0) cc_final: 0.8436 (t0) REVERT: D 743 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8158 (mtp85) REVERT: D 996 CYS cc_start: 0.8797 (p) cc_final: 0.8513 (p) outliers start: 1 outliers final: 0 residues processed: 443 average time/residue: 0.2563 time to fit residues: 173.8444 Evaluate side-chains 354 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 43 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 ASN B 904 GLN B1006 GLN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** D 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087852 restraints weight = 61523.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090160 restraints weight = 42006.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091880 restraints weight = 31580.965| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17074 Z= 0.176 Angle : 0.638 7.641 23155 Z= 0.340 Chirality : 0.044 0.175 2669 Planarity : 0.005 0.077 3004 Dihedral : 4.815 22.763 2346 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.31 % Favored : 90.46 % Rotamer: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2181 helix: 0.56 (0.17), residues: 968 sheet: 0.25 (0.40), residues: 176 loop : -2.62 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 266 HIS 0.006 0.001 HIS C 109 PHE 0.036 0.002 PHE B1023 TYR 0.014 0.002 TYR D 649 ARG 0.010 0.001 ARG B 933 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 696) hydrogen bonds : angle 4.35513 ( 1995) covalent geometry : bond 0.00385 (17074) covalent geometry : angle 0.63828 (23155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 433 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9230 (mmm) cc_final: 0.9016 (mmm) REVERT: A 110 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8690 (mm-40) REVERT: A 177 ASN cc_start: 0.9478 (t0) cc_final: 0.9261 (t0) REVERT: A 199 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 105 GLU cc_start: 0.5377 (pp20) cc_final: 0.5021 (pp20) REVERT: B 140 LEU cc_start: 0.8556 (mm) cc_final: 0.8191 (mm) REVERT: B 248 TRP cc_start: 0.8532 (m100) cc_final: 0.7601 (m100) REVERT: B 249 VAL cc_start: 0.9438 (t) cc_final: 0.9235 (t) REVERT: B 251 PHE cc_start: 0.8767 (m-80) cc_final: 0.7807 (m-80) REVERT: B 264 VAL cc_start: 0.8871 (t) cc_final: 0.8579 (t) REVERT: B 347 MET cc_start: 0.8870 (ptp) cc_final: 0.8530 (ptt) REVERT: B 398 ASP cc_start: 0.8904 (m-30) cc_final: 0.8118 (m-30) REVERT: B 402 TYR cc_start: 0.8954 (m-80) cc_final: 0.8738 (m-80) REVERT: B 406 MET cc_start: 0.8930 (mmp) cc_final: 0.8631 (mmm) REVERT: B 456 HIS cc_start: 0.8667 (p90) cc_final: 0.8104 (p-80) REVERT: B 460 LEU cc_start: 0.9420 (mt) cc_final: 0.9127 (mt) REVERT: B 538 MET cc_start: 0.8848 (ppp) cc_final: 0.7976 (ppp) REVERT: B 560 ASN cc_start: 0.8616 (m110) cc_final: 0.8413 (m110) REVERT: B 700 LEU cc_start: 0.9633 (mm) cc_final: 0.9408 (mm) REVERT: B 944 LYS cc_start: 0.9401 (mmtm) cc_final: 0.9181 (mmmt) REVERT: B 958 TYR cc_start: 0.9013 (t80) cc_final: 0.8799 (t80) REVERT: B 979 PHE cc_start: 0.8985 (t80) cc_final: 0.8424 (t80) REVERT: B 999 ARG cc_start: 0.8901 (mpp-170) cc_final: 0.8684 (mpp-170) REVERT: B 1007 MET cc_start: 0.9355 (mmp) cc_final: 0.9014 (tpt) REVERT: B 1023 PHE cc_start: 0.9122 (m-80) cc_final: 0.8806 (m-80) REVERT: C 104 ILE cc_start: 0.8796 (mp) cc_final: 0.8227 (mm) REVERT: C 136 PHE cc_start: 0.8799 (m-10) cc_final: 0.8378 (t80) REVERT: C 138 LEU cc_start: 0.8927 (mm) cc_final: 0.8440 (mm) REVERT: C 185 GLN cc_start: 0.9027 (mp10) cc_final: 0.8699 (mp10) REVERT: D 122 TYR cc_start: 0.8388 (p90) cc_final: 0.8047 (t80) REVERT: D 212 MET cc_start: -0.0260 (tpt) cc_final: -0.1414 (mmt) REVERT: D 281 PHE cc_start: 0.8181 (m-10) cc_final: 0.7935 (m-10) REVERT: D 308 TYR cc_start: 0.7489 (t80) cc_final: 0.7241 (t80) REVERT: D 676 ASN cc_start: 0.8969 (t0) cc_final: 0.8635 (t0) REVERT: D 743 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8343 (mmm-85) REVERT: D 996 CYS cc_start: 0.8812 (p) cc_final: 0.8513 (p) outliers start: 2 outliers final: 0 residues processed: 434 average time/residue: 0.2468 time to fit residues: 164.3186 Evaluate side-chains 359 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 218 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 173 optimal weight: 0.1980 chunk 145 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 95 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 185 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 440 GLN B 572 ASN B 904 GLN B1006 GLN B1009 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** D 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.132618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092132 restraints weight = 58908.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094408 restraints weight = 40954.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095935 restraints weight = 31188.607| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17074 Z= 0.112 Angle : 0.602 7.618 23155 Z= 0.315 Chirality : 0.044 0.163 2669 Planarity : 0.004 0.078 3004 Dihedral : 4.623 23.033 2346 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.67 % Favored : 91.10 % Rotamer: Outliers : 0.12 % Allowed : 2.08 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2181 helix: 0.66 (0.17), residues: 971 sheet: 0.53 (0.41), residues: 170 loop : -2.60 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 266 HIS 0.008 0.001 HIS B 318 PHE 0.030 0.001 PHE B1023 TYR 0.015 0.001 TYR B 256 ARG 0.006 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 696) hydrogen bonds : angle 4.13432 ( 1995) covalent geometry : bond 0.00249 (17074) covalent geometry : angle 0.60189 (23155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.9597 (mt) cc_final: 0.9364 (mp) REVERT: A 110 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8663 (mm-40) REVERT: A 177 ASN cc_start: 0.9458 (t0) cc_final: 0.9225 (t0) REVERT: A 199 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 248 TRP cc_start: 0.8475 (m100) cc_final: 0.7708 (m100) REVERT: B 251 PHE cc_start: 0.8656 (m-80) cc_final: 0.7814 (m-80) REVERT: B 257 MET cc_start: 0.7286 (mmp) cc_final: 0.6358 (mmp) REVERT: B 347 MET cc_start: 0.8889 (ptp) cc_final: 0.8566 (ptt) REVERT: B 406 MET cc_start: 0.8896 (mmp) cc_final: 0.8609 (mmm) REVERT: B 456 HIS cc_start: 0.8876 (p90) cc_final: 0.8395 (p-80) REVERT: B 460 LEU cc_start: 0.9394 (mt) cc_final: 0.9120 (mt) REVERT: B 538 MET cc_start: 0.8885 (ppp) cc_final: 0.8081 (ppp) REVERT: B 560 ASN cc_start: 0.8582 (m110) cc_final: 0.8381 (m110) REVERT: B 944 LYS cc_start: 0.9396 (mmtm) cc_final: 0.9168 (mmmt) REVERT: B 958 TYR cc_start: 0.8935 (t80) cc_final: 0.8730 (t80) REVERT: C 73 LYS cc_start: 0.9158 (mppt) cc_final: 0.8677 (mptt) REVERT: C 136 PHE cc_start: 0.8773 (m-10) cc_final: 0.8314 (t80) REVERT: C 138 LEU cc_start: 0.8888 (mm) cc_final: 0.8352 (mm) REVERT: C 172 VAL cc_start: 0.9128 (m) cc_final: 0.8389 (m) REVERT: C 185 GLN cc_start: 0.8954 (mp10) cc_final: 0.8598 (mp10) REVERT: C 203 TYR cc_start: 0.8000 (p90) cc_final: 0.7752 (p90) REVERT: C 205 GLN cc_start: 0.8804 (tm-30) cc_final: 0.7871 (pm20) REVERT: D 122 TYR cc_start: 0.8405 (p90) cc_final: 0.8051 (t80) REVERT: D 202 MET cc_start: 0.8371 (ptp) cc_final: 0.7941 (ptp) REVERT: D 212 MET cc_start: -0.0397 (tpt) cc_final: -0.1446 (mmt) REVERT: D 281 PHE cc_start: 0.8163 (m-10) cc_final: 0.7886 (m-10) REVERT: D 308 TYR cc_start: 0.7384 (t80) cc_final: 0.7132 (t80) REVERT: D 512 ILE cc_start: 0.7875 (pt) cc_final: 0.7666 (pt) REVERT: D 520 MET cc_start: 0.8776 (mmm) cc_final: 0.8028 (ptp) REVERT: D 676 ASN cc_start: 0.8862 (t0) cc_final: 0.8549 (t0) REVERT: D 985 MET cc_start: 0.7885 (mpp) cc_final: 0.7078 (pmm) REVERT: D 996 CYS cc_start: 0.8837 (p) cc_final: 0.8537 (p) outliers start: 2 outliers final: 0 residues processed: 448 average time/residue: 0.2639 time to fit residues: 179.5088 Evaluate side-chains 363 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 38 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 21 optimal weight: 0.0050 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 568 ASN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.131747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091580 restraints weight = 58722.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093862 restraints weight = 40616.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095512 restraints weight = 30787.799| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17074 Z= 0.120 Angle : 0.605 7.888 23155 Z= 0.319 Chirality : 0.044 0.181 2669 Planarity : 0.004 0.080 3004 Dihedral : 4.599 22.111 2346 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.57 % Favored : 91.20 % Rotamer: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2181 helix: 0.62 (0.17), residues: 973 sheet: 0.36 (0.40), residues: 182 loop : -2.55 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 266 HIS 0.010 0.001 HIS D 594 PHE 0.011 0.001 PHE A 166 TYR 0.018 0.001 TYR B 136 ARG 0.005 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 696) hydrogen bonds : angle 4.18971 ( 1995) covalent geometry : bond 0.00267 (17074) covalent geometry : angle 0.60520 (23155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.9485 (t0) cc_final: 0.9259 (t0) REVERT: A 179 CYS cc_start: 0.8225 (m) cc_final: 0.8025 (m) REVERT: A 199 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 105 GLU cc_start: 0.5507 (pp20) cc_final: 0.5124 (pp20) REVERT: B 248 TRP cc_start: 0.8527 (m100) cc_final: 0.7658 (m100) REVERT: B 249 VAL cc_start: 0.9453 (t) cc_final: 0.9218 (t) REVERT: B 251 PHE cc_start: 0.8733 (m-80) cc_final: 0.7915 (m-80) REVERT: B 257 MET cc_start: 0.7054 (mmp) cc_final: 0.5713 (mmp) REVERT: B 347 MET cc_start: 0.8867 (ptp) cc_final: 0.8527 (ptt) REVERT: B 402 TYR cc_start: 0.8945 (m-80) cc_final: 0.8718 (m-80) REVERT: B 406 MET cc_start: 0.8952 (mmp) cc_final: 0.8641 (mmm) REVERT: B 456 HIS cc_start: 0.8882 (p90) cc_final: 0.8392 (p-80) REVERT: B 460 LEU cc_start: 0.9426 (mt) cc_final: 0.9152 (mt) REVERT: B 538 MET cc_start: 0.8907 (ppp) cc_final: 0.8069 (ppp) REVERT: B 560 ASN cc_start: 0.8547 (m110) cc_final: 0.8346 (m110) REVERT: B 743 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7153 (ttm-80) REVERT: B 944 LYS cc_start: 0.9393 (mmtm) cc_final: 0.9161 (mmmt) REVERT: B 979 PHE cc_start: 0.8987 (t80) cc_final: 0.8400 (t80) REVERT: B 1031 LYS cc_start: 0.8852 (mppt) cc_final: 0.8554 (tppt) REVERT: C 71 LYS cc_start: 0.9091 (pptt) cc_final: 0.8872 (pptt) REVERT: C 104 ILE cc_start: 0.8768 (mp) cc_final: 0.8478 (mm) REVERT: C 110 GLN cc_start: 0.9424 (mp10) cc_final: 0.9136 (mp10) REVERT: C 113 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9255 (mt-10) REVERT: C 136 PHE cc_start: 0.8793 (m-10) cc_final: 0.8338 (t80) REVERT: C 138 LEU cc_start: 0.8906 (mm) cc_final: 0.8466 (mm) REVERT: C 185 GLN cc_start: 0.8950 (mp10) cc_final: 0.8532 (mp10) REVERT: C 203 TYR cc_start: 0.8042 (p90) cc_final: 0.7698 (p90) REVERT: C 205 GLN cc_start: 0.8724 (tm-30) cc_final: 0.7843 (pm20) REVERT: D 122 TYR cc_start: 0.8409 (p90) cc_final: 0.8049 (t80) REVERT: D 202 MET cc_start: 0.8505 (ptp) cc_final: 0.8110 (ptp) REVERT: D 212 MET cc_start: -0.0288 (tpt) cc_final: -0.1342 (mmt) REVERT: D 216 VAL cc_start: 0.5834 (t) cc_final: 0.5633 (t) REVERT: D 268 GLU cc_start: 0.8601 (tp30) cc_final: 0.8350 (tp30) REVERT: D 281 PHE cc_start: 0.8244 (m-10) cc_final: 0.7959 (m-10) REVERT: D 308 TYR cc_start: 0.7364 (t80) cc_final: 0.7126 (t80) REVERT: D 520 MET cc_start: 0.8749 (mmm) cc_final: 0.8005 (ptp) REVERT: D 538 MET cc_start: 0.6644 (mmp) cc_final: 0.6281 (mmp) REVERT: D 668 ASP cc_start: 0.6847 (t0) cc_final: 0.6640 (t0) REVERT: D 676 ASN cc_start: 0.8884 (t0) cc_final: 0.8562 (t0) REVERT: D 985 MET cc_start: 0.7734 (mpp) cc_final: 0.6954 (pmm) REVERT: D 996 CYS cc_start: 0.8800 (p) cc_final: 0.8499 (p) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.2634 time to fit residues: 175.9697 Evaluate side-chains 357 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 54 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 440 GLN B 519 GLN B 568 ASN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091133 restraints weight = 60964.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093501 restraints weight = 41684.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095197 restraints weight = 31195.252| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17074 Z= 0.119 Angle : 0.622 8.969 23155 Z= 0.324 Chirality : 0.044 0.157 2669 Planarity : 0.004 0.081 3004 Dihedral : 4.584 22.110 2346 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.57 % Favored : 91.20 % Rotamer: Outliers : 0.12 % Allowed : 1.21 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2181 helix: 0.68 (0.17), residues: 972 sheet: 0.38 (0.40), residues: 182 loop : -2.52 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 266 HIS 0.009 0.001 HIS D 594 PHE 0.013 0.001 PHE D 509 TYR 0.013 0.001 TYR B 256 ARG 0.006 0.000 ARG D 743 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 696) hydrogen bonds : angle 4.15963 ( 1995) covalent geometry : bond 0.00267 (17074) covalent geometry : angle 0.62237 (23155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 441 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8585 (tp40) cc_final: 0.8179 (tp-100) REVERT: A 110 GLN cc_start: 0.9105 (mp-120) cc_final: 0.8643 (tp40) REVERT: A 177 ASN cc_start: 0.9451 (t0) cc_final: 0.9245 (t0) REVERT: A 199 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 105 GLU cc_start: 0.5672 (pp20) cc_final: 0.5324 (pp20) REVERT: B 146 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 248 TRP cc_start: 0.8518 (m100) cc_final: 0.7466 (m100) REVERT: B 249 VAL cc_start: 0.9455 (t) cc_final: 0.9220 (t) REVERT: B 251 PHE cc_start: 0.8728 (m-80) cc_final: 0.7950 (m-80) REVERT: B 257 MET cc_start: 0.7086 (mmp) cc_final: 0.5718 (mmp) REVERT: B 347 MET cc_start: 0.8847 (ptp) cc_final: 0.8505 (ptt) REVERT: B 406 MET cc_start: 0.8933 (mmp) cc_final: 0.8635 (mmm) REVERT: B 456 HIS cc_start: 0.8805 (p90) cc_final: 0.8356 (p-80) REVERT: B 460 LEU cc_start: 0.9421 (mt) cc_final: 0.9156 (mt) REVERT: B 475 LEU cc_start: 0.7595 (mp) cc_final: 0.7317 (mp) REVERT: B 482 THR cc_start: 0.6262 (m) cc_final: 0.6038 (m) REVERT: B 519 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8604 (tm-30) REVERT: B 538 MET cc_start: 0.8858 (ppp) cc_final: 0.8042 (ppp) REVERT: B 560 ASN cc_start: 0.8535 (m110) cc_final: 0.8321 (m110) REVERT: B 743 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.7293 (ttm-80) REVERT: B 933 ARG cc_start: 0.9301 (ptp-170) cc_final: 0.8872 (tpp80) REVERT: B 944 LYS cc_start: 0.9401 (mmtm) cc_final: 0.9163 (mmmt) REVERT: B 979 PHE cc_start: 0.8979 (t80) cc_final: 0.8388 (t80) REVERT: C 71 LYS cc_start: 0.9085 (pptt) cc_final: 0.8872 (pptt) REVERT: C 104 ILE cc_start: 0.8730 (mp) cc_final: 0.8511 (mm) REVERT: C 136 PHE cc_start: 0.8830 (m-10) cc_final: 0.8276 (t80) REVERT: C 138 LEU cc_start: 0.8929 (mm) cc_final: 0.8413 (mm) REVERT: C 185 GLN cc_start: 0.9012 (mp10) cc_final: 0.8744 (mp10) REVERT: C 203 TYR cc_start: 0.7996 (p90) cc_final: 0.7722 (p90) REVERT: C 205 GLN cc_start: 0.8713 (tm-30) cc_final: 0.7964 (pm20) REVERT: D 122 TYR cc_start: 0.8398 (p90) cc_final: 0.8023 (t80) REVERT: D 202 MET cc_start: 0.8558 (ptp) cc_final: 0.8166 (ptp) REVERT: D 212 MET cc_start: -0.0469 (tpt) cc_final: -0.1508 (mmt) REVERT: D 268 GLU cc_start: 0.8685 (tp30) cc_final: 0.8385 (tp30) REVERT: D 281 PHE cc_start: 0.8233 (m-10) cc_final: 0.7988 (m-10) REVERT: D 512 ILE cc_start: 0.7975 (pt) cc_final: 0.7764 (pt) REVERT: D 520 MET cc_start: 0.8726 (mmm) cc_final: 0.7993 (ptp) REVERT: D 538 MET cc_start: 0.6620 (mmp) cc_final: 0.6334 (mmp) REVERT: D 676 ASN cc_start: 0.8907 (t0) cc_final: 0.8591 (t0) REVERT: D 985 MET cc_start: 0.7744 (mpp) cc_final: 0.6987 (pmm) REVERT: D 996 CYS cc_start: 0.8711 (p) cc_final: 0.8373 (p) outliers start: 2 outliers final: 0 residues processed: 441 average time/residue: 0.2787 time to fit residues: 186.8140 Evaluate side-chains 361 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3694 > 50: distance: 20 - 24: 10.842 distance: 24 - 25: 12.644 distance: 25 - 26: 17.635 distance: 25 - 28: 6.816 distance: 26 - 27: 5.590 distance: 26 - 33: 22.001 distance: 28 - 29: 4.680 distance: 29 - 30: 11.850 distance: 30 - 31: 10.205 distance: 30 - 32: 6.128 distance: 33 - 34: 16.137 distance: 34 - 35: 8.438 distance: 34 - 37: 30.175 distance: 35 - 36: 45.690 distance: 35 - 39: 23.660 distance: 37 - 38: 43.623 distance: 39 - 40: 15.140 distance: 40 - 41: 25.948 distance: 40 - 43: 19.041 distance: 41 - 42: 27.799 distance: 41 - 46: 17.276 distance: 42 - 133: 37.432 distance: 43 - 44: 13.039 distance: 43 - 45: 15.440 distance: 46 - 47: 20.565 distance: 47 - 48: 61.153 distance: 47 - 50: 39.607 distance: 48 - 49: 39.317 distance: 48 - 54: 35.002 distance: 50 - 51: 40.293 distance: 51 - 52: 26.063 distance: 51 - 53: 3.586 distance: 54 - 55: 33.894 distance: 54 - 136: 13.422 distance: 55 - 56: 20.328 distance: 55 - 58: 32.264 distance: 56 - 57: 38.308 distance: 56 - 61: 21.938 distance: 57 - 147: 36.163 distance: 58 - 59: 38.412 distance: 58 - 60: 33.068 distance: 61 - 62: 15.461 distance: 62 - 63: 25.738 distance: 62 - 65: 25.295 distance: 63 - 64: 17.815 distance: 63 - 67: 26.979 distance: 65 - 66: 28.738 distance: 67 - 68: 9.151 distance: 68 - 69: 13.487 distance: 68 - 71: 35.168 distance: 69 - 70: 12.910 distance: 69 - 72: 41.190 distance: 72 - 73: 19.257 distance: 73 - 74: 11.393 distance: 73 - 76: 6.314 distance: 74 - 75: 17.673 distance: 74 - 82: 9.219 distance: 75 - 95: 18.693 distance: 76 - 77: 22.596 distance: 77 - 78: 24.494 distance: 77 - 79: 32.204 distance: 78 - 80: 19.407 distance: 79 - 81: 8.393 distance: 80 - 81: 22.448 distance: 82 - 83: 25.713 distance: 83 - 84: 17.458 distance: 83 - 86: 40.861 distance: 84 - 85: 11.932 distance: 84 - 89: 19.181 distance: 86 - 87: 12.387 distance: 86 - 88: 35.513 distance: 89 - 90: 9.567 distance: 90 - 91: 43.653 distance: 90 - 93: 22.310 distance: 91 - 92: 40.651 distance: 91 - 95: 27.095 distance: 93 - 94: 20.568