Starting phenix.real_space_refine on Wed Mar 4 22:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4y_14510/03_2026/7z4y_14510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4y_14510/03_2026/7z4y_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z4y_14510/03_2026/7z4y_14510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4y_14510/03_2026/7z4y_14510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4y_14510/03_2026/7z4y_14510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4y_14510/03_2026/7z4y_14510.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 3, 'PHE:plan': 1} 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: {'ARG:plan': 4, 'GLU:plan': 12, 'ASN:plan1': 6, 'GLN:plan1': 3, 'ASP:plan': 5, 'HIS:plan': 1} 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: {'ASP:plan': 3, 'GLU:plan': 14, 'ARG:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 4} 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: {'ARG:plan': 4, 'GLU:plan': 15, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 3.98, per 1000 atoms: 0.24 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: 1.45 Conformation dependent library (CDL) restraints added in 844.8 milliseconds 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: 0.57 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: 3.08 Time building geometry restraints manager: 1.90 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: 3.860 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 16.410 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- 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 : 14.92 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG B 933 TYR 0.028 0.001 TYR A 108 PHE 0.023 0.002 PHE A 115 TRP 0.029 0.002 TRP B 266 HIS 0.007 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00331 (17074) covalent geometry : angle 0.74051 (23155) hydrogen bonds : bond 0.20147 ( 696) hydrogen bonds : angle 6.67388 ( 1995) *********************** 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 : 0.689 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: 0.1205 time to fit residues: 82.8961 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 : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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** C 209 HIS D 300 HIS D 568 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.130286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090170 restraints weight = 60896.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092539 restraints weight = 40945.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094268 restraints weight = 30911.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095139 restraints weight = 25024.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096113 restraints weight = 21985.667| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17074 Z= 0.190 Angle : 0.659 8.161 23155 Z= 0.352 Chirality : 0.044 0.156 2669 Planarity : 0.005 0.062 3004 Dihedral : 4.908 22.808 2346 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.08 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.18), residues: 2181 helix: 0.49 (0.17), residues: 952 sheet: 0.40 (0.39), residues: 182 loop : -2.85 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 262 TYR 0.012 0.001 TYR B 256 PHE 0.017 0.002 PHE A 166 TRP 0.014 0.001 TRP D 266 HIS 0.009 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00406 (17074) covalent geometry : angle 0.65921 (23155) hydrogen bonds : bond 0.04763 ( 696) hydrogen bonds : angle 4.96150 ( 1995) *********************** 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 438 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.650 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 71 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8528 (mmtm) REVERT: A 75 ASN cc_start: 0.9234 (m-40) cc_final: 0.8736 (m-40) REVERT: A 95 LEU cc_start: 0.9142 (mp) cc_final: 0.8879 (mp) REVERT: A 179 CYS cc_start: 0.8019 (m) cc_final: 0.7716 (m) REVERT: A 199 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 140 LEU cc_start: 0.8933 (mm) cc_final: 0.8550 (mm) REVERT: B 253 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 257 MET cc_start: 0.7600 (mmm) cc_final: 0.6976 (mmt) REVERT: B 347 MET cc_start: 0.8821 (ptp) cc_final: 0.8533 (ptt) REVERT: B 402 TYR cc_start: 0.8930 (m-80) cc_final: 0.8716 (m-80) REVERT: B 456 HIS cc_start: 0.8862 (p90) cc_final: 0.8190 (p-80) REVERT: B 538 MET cc_start: 0.8770 (ppp) cc_final: 0.8010 (ppp) REVERT: B 650 CYS cc_start: 0.8081 (p) cc_final: 0.7880 (p) REVERT: B 658 ARG cc_start: 0.7785 (mmp-170) cc_final: 0.7415 (mmp-170) REVERT: B 700 LEU cc_start: 0.9571 (mm) cc_final: 0.9314 (mm) REVERT: B 958 TYR cc_start: 0.9139 (t80) cc_final: 0.8891 (t80) REVERT: B 967 MET cc_start: 0.8334 (mpp) cc_final: 0.7965 (mpp) REVERT: B 979 PHE cc_start: 0.8923 (t80) cc_final: 0.8302 (t80) REVERT: B 1007 MET cc_start: 0.9350 (mmp) cc_final: 0.9111 (mmp) REVERT: C 185 GLN cc_start: 0.9068 (mp10) cc_final: 0.8856 (mp10) REVERT: D 122 TYR cc_start: 0.8535 (p90) cc_final: 0.8193 (t80) REVERT: D 212 MET cc_start: -0.0184 (tpt) cc_final: -0.1282 (mmt) REVERT: D 281 PHE cc_start: 0.8199 (m-10) cc_final: 0.7974 (m-10) REVERT: D 296 ILE cc_start: 0.9494 (mm) cc_final: 0.9276 (mm) REVERT: D 308 TYR cc_start: 0.7556 (t80) cc_final: 0.7253 (t80) REVERT: D 676 ASN cc_start: 0.8846 (t0) cc_final: 0.8536 (t0) REVERT: D 921 MET cc_start: 0.0116 (tpt) cc_final: -0.0276 (tpt) REVERT: D 940 LYS cc_start: 0.9288 (pptt) cc_final: 0.9066 (tptt) REVERT: D 985 MET cc_start: 0.7985 (mpp) cc_final: 0.7310 (pmm) REVERT: D 1031 LYS cc_start: 0.8572 (pttm) cc_final: 0.8040 (tptt) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1252 time to fit residues: 85.3138 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 : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.0470 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092937 restraints weight = 61326.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095405 restraints weight = 41568.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097184 restraints weight = 31315.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098398 restraints weight = 25355.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099242 restraints weight = 21697.237| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1969 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= 0.118 Angle : 0.597 8.613 23155 Z= 0.317 Chirality : 0.044 0.158 2669 Planarity : 0.004 0.068 3004 Dihedral : 4.797 25.082 2346 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.30 % Favored : 91.47 % Rotamer: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 2181 helix: 0.64 (0.17), residues: 950 sheet: 0.50 (0.39), residues: 181 loop : -2.71 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 262 TYR 0.015 0.001 TYR B 256 PHE 0.039 0.001 PHE B1023 TRP 0.014 0.002 TRP B 266 HIS 0.008 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00258 (17074) covalent geometry : angle 0.59743 (23155) hydrogen bonds : bond 0.03743 ( 696) hydrogen bonds : angle 4.42485 ( 1995) *********************** 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 450 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 0.644 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: 0.9074 (mmtm) cc_final: 0.8504 (mmtm) REVERT: A 75 ASN cc_start: 0.9274 (m-40) cc_final: 0.8845 (m-40) REVERT: A 177 ASN cc_start: 0.9345 (t0) cc_final: 0.9098 (t0) REVERT: A 179 CYS cc_start: 0.7895 (m) cc_final: 0.7610 (m) REVERT: A 199 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 140 LEU cc_start: 0.8911 (mm) cc_final: 0.8528 (mm) REVERT: B 257 MET cc_start: 0.7742 (mmm) cc_final: 0.7255 (mmt) REVERT: B 347 MET cc_start: 0.8841 (ptp) cc_final: 0.8516 (ptt) REVERT: B 456 HIS cc_start: 0.8859 (p90) cc_final: 0.8173 (p-80) REVERT: B 460 LEU cc_start: 0.9459 (mt) cc_final: 0.9206 (mt) REVERT: B 538 MET cc_start: 0.8835 (ppp) cc_final: 0.8067 (ppp) REVERT: B 566 THR cc_start: 0.9285 (t) cc_final: 0.8934 (p) REVERT: B 778 ASP cc_start: 0.8231 (t70) cc_final: 0.8007 (t70) REVERT: B 944 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9105 (mmmt) REVERT: B 958 TYR cc_start: 0.9131 (t80) cc_final: 0.8865 (t80) REVERT: B 1007 MET cc_start: 0.9386 (mmp) cc_final: 0.9130 (mmp) REVERT: C 181 ASP cc_start: 0.8838 (t0) cc_final: 0.8626 (t0) REVERT: C 185 GLN cc_start: 0.9134 (mp10) cc_final: 0.8822 (mp10) REVERT: D 122 TYR cc_start: 0.8454 (p90) cc_final: 0.8124 (t80) REVERT: D 212 MET cc_start: -0.0488 (tpt) cc_final: -0.1676 (mmt) REVERT: D 281 PHE cc_start: 0.8068 (m-10) cc_final: 0.7864 (m-10) REVERT: D 308 TYR cc_start: 0.7526 (t80) cc_final: 0.7270 (t80) REVERT: D 676 ASN cc_start: 0.8804 (t0) cc_final: 0.8397 (t0) REVERT: D 940 LYS cc_start: 0.9323 (pptt) cc_final: 0.9094 (tptt) REVERT: D 994 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7255 (mt) REVERT: D 996 CYS cc_start: 0.8748 (p) cc_final: 0.8455 (p) REVERT: D 1030 ILE cc_start: 0.9192 (pt) cc_final: 0.8985 (pt) REVERT: D 1031 LYS cc_start: 0.8539 (pttm) cc_final: 0.8031 (tptt) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.1233 time to fit residues: 86.0437 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 : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 0.0570 overall best weight: 2.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 ASN B 904 GLN B1006 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 298 HIS D 655 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 = 0.3922 r_free = 0.3922 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084911 restraints weight = 61664.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086794 restraints weight = 42342.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088437 restraints weight = 32959.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089234 restraints weight = 26909.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090047 restraints weight = 23890.543| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17074 Z= 0.254 Angle : 0.762 10.676 23155 Z= 0.402 Chirality : 0.047 0.228 2669 Planarity : 0.006 0.076 3004 Dihedral : 5.401 26.766 2346 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.73 % Favored : 89.04 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2181 helix: 0.14 (0.16), residues: 985 sheet: 0.11 (0.39), residues: 185 loop : -2.79 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 933 TYR 0.021 0.002 TYR D 649 PHE 0.024 0.002 PHE A 166 TRP 0.021 0.002 TRP B 266 HIS 0.014 0.002 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00537 (17074) covalent geometry : angle 0.76218 (23155) hydrogen bonds : bond 0.04269 ( 696) hydrogen bonds : angle 4.85168 ( 1995) *********************** 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 420 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.610 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: 0.9033 (mmtm) cc_final: 0.8451 (mmtm) REVERT: A 75 ASN cc_start: 0.9218 (m-40) cc_final: 0.8778 (m-40) REVERT: A 110 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8899 (tp-100) REVERT: A 145 ILE cc_start: 0.8385 (pt) cc_final: 0.8138 (tp) REVERT: A 177 ASN cc_start: 0.9447 (t0) cc_final: 0.9229 (t0) REVERT: A 199 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 105 GLU cc_start: 0.5240 (pp20) cc_final: 0.4905 (pp20) REVERT: B 140 LEU cc_start: 0.8916 (mm) cc_final: 0.8559 (mm) REVERT: B 264 VAL cc_start: 0.8690 (t) cc_final: 0.8282 (t) REVERT: B 291 GLN cc_start: 0.9294 (mp10) cc_final: 0.9077 (mp10) REVERT: B 347 MET cc_start: 0.8855 (ptp) cc_final: 0.8389 (ptt) REVERT: B 406 MET cc_start: 0.8919 (mmp) cc_final: 0.8624 (mmm) REVERT: B 456 HIS cc_start: 0.8621 (p90) cc_final: 0.8400 (p-80) REVERT: B 538 MET cc_start: 0.8843 (ppp) cc_final: 0.7971 (ppp) REVERT: B 560 ASN cc_start: 0.8702 (m110) cc_final: 0.8497 (m110) REVERT: B 654 LEU cc_start: 0.9618 (mt) cc_final: 0.9381 (mt) REVERT: B 944 LYS cc_start: 0.9428 (mmpt) cc_final: 0.9123 (mmmt) REVERT: B 979 PHE cc_start: 0.8852 (t80) cc_final: 0.8400 (t80) REVERT: B 985 MET cc_start: 0.8037 (pmm) cc_final: 0.7464 (pmm) REVERT: B 1007 MET cc_start: 0.9333 (mmp) cc_final: 0.9092 (mmp) REVERT: C 96 GLN cc_start: 0.7825 (tp40) cc_final: 0.7558 (tp-100) REVERT: C 100 MET cc_start: 0.8635 (mmm) cc_final: 0.8262 (mmm) REVERT: C 136 PHE cc_start: 0.8813 (m-10) cc_final: 0.8429 (t80) REVERT: C 138 LEU cc_start: 0.9018 (mm) cc_final: 0.8682 (mm) REVERT: C 181 ASP cc_start: 0.8989 (t0) cc_final: 0.8432 (t0) REVERT: C 185 GLN cc_start: 0.9054 (mp10) cc_final: 0.8764 (mp10) REVERT: D 122 TYR cc_start: 0.8369 (p90) cc_final: 0.8034 (t80) REVERT: D 212 MET cc_start: -0.0012 (tpt) cc_final: -0.1285 (mmt) REVERT: D 281 PHE cc_start: 0.8330 (m-10) cc_final: 0.8114 (m-10) REVERT: D 308 TYR cc_start: 0.7474 (t80) cc_final: 0.7192 (t80) REVERT: D 382 MET cc_start: 0.7961 (mmp) cc_final: 0.7675 (mmp) REVERT: D 676 ASN cc_start: 0.9070 (t0) cc_final: 0.8817 (t0) REVERT: D 743 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8558 (mtm110) REVERT: D 888 LEU cc_start: 0.4627 (mt) cc_final: 0.4352 (mt) REVERT: D 940 LYS cc_start: 0.9274 (pptt) cc_final: 0.9043 (tptt) REVERT: D 996 CYS cc_start: 0.8793 (p) cc_final: 0.8486 (p) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1223 time to fit residues: 79.6545 Evaluate side-chains 338 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 36 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 192 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 210 optimal weight: 0.0010 chunk 178 optimal weight: 0.0670 chunk 172 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 568 ASN 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 412 ASN 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 = 0.3985 r_free = 0.3985 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090911 restraints weight = 58470.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093198 restraints weight = 39659.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094845 restraints weight = 30222.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095956 restraints weight = 24659.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096625 restraints weight = 21282.368| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17074 Z= 0.120 Angle : 0.621 8.341 23155 Z= 0.328 Chirality : 0.044 0.160 2669 Planarity : 0.004 0.077 3004 Dihedral : 4.951 23.983 2346 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.57 % Favored : 91.20 % Rotamer: Outliers : 0.23 % Allowed : 2.78 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.18), residues: 2181 helix: 0.47 (0.17), residues: 974 sheet: 0.47 (0.41), residues: 161 loop : -2.64 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.014 0.001 TYR D 517 PHE 0.015 0.001 PHE D 509 TRP 0.017 0.001 TRP B 266 HIS 0.009 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00261 (17074) covalent geometry : angle 0.62053 (23155) hydrogen bonds : bond 0.03486 ( 696) hydrogen bonds : angle 4.30097 ( 1995) *********************** 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 465 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 461 time to evaluate : 0.645 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: 0.9021 (mmtm) cc_final: 0.8786 (mmtm) REVERT: A 96 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8503 (tp40) REVERT: A 97 ILE cc_start: 0.9530 (mt) cc_final: 0.9240 (mp) REVERT: A 177 ASN cc_start: 0.9434 (t0) cc_final: 0.9192 (t0) REVERT: A 199 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 140 LEU cc_start: 0.8916 (mm) cc_final: 0.8552 (mm) REVERT: B 248 TRP cc_start: 0.8525 (m100) cc_final: 0.7640 (m100) REVERT: B 257 MET cc_start: 0.8443 (mtm) cc_final: 0.8092 (mtt) REVERT: B 264 VAL cc_start: 0.8752 (t) cc_final: 0.8292 (t) REVERT: B 267 GLU cc_start: 0.8822 (mp0) cc_final: 0.8565 (mp0) REVERT: B 347 MET cc_start: 0.8873 (ptp) cc_final: 0.8537 (ptt) REVERT: B 406 MET cc_start: 0.8886 (mmp) cc_final: 0.8615 (mmm) REVERT: B 456 HIS cc_start: 0.8738 (p90) cc_final: 0.8064 (p-80) REVERT: B 460 LEU cc_start: 0.9342 (mt) cc_final: 0.9024 (mt) REVERT: B 520 MET cc_start: 0.8623 (mmt) cc_final: 0.8370 (mmt) REVERT: B 538 MET cc_start: 0.8912 (ppp) cc_final: 0.8080 (ppp) REVERT: B 560 ASN cc_start: 0.8604 (m110) cc_final: 0.8383 (m110) REVERT: B 933 ARG cc_start: 0.9265 (mpp-170) cc_final: 0.8851 (tpp80) REVERT: B 944 LYS cc_start: 0.9451 (mmpt) cc_final: 0.9119 (mmmt) REVERT: B 1007 MET cc_start: 0.9375 (mmp) cc_final: 0.9117 (mmp) REVERT: C 136 PHE cc_start: 0.8781 (m-10) cc_final: 0.8356 (t80) REVERT: C 138 LEU cc_start: 0.8980 (mm) cc_final: 0.8531 (mm) REVERT: C 172 VAL cc_start: 0.9021 (m) cc_final: 0.8506 (m) REVERT: C 185 GLN cc_start: 0.9022 (mp10) cc_final: 0.8642 (mp10) REVERT: D 122 TYR cc_start: 0.8396 (p90) cc_final: 0.8043 (t80) REVERT: D 202 MET cc_start: 0.8410 (ptp) cc_final: 0.7979 (ptp) REVERT: D 212 MET cc_start: -0.1543 (tpt) cc_final: -0.2020 (mmt) REVERT: D 281 PHE cc_start: 0.8200 (m-10) cc_final: 0.7972 (m-10) REVERT: D 308 TYR cc_start: 0.7318 (t80) cc_final: 0.7040 (t80) REVERT: D 412 ASN cc_start: 0.4259 (OUTLIER) cc_final: 0.3980 (p0) REVERT: D 676 ASN cc_start: 0.8967 (t0) cc_final: 0.8429 (t0) REVERT: D 985 MET cc_start: 0.7725 (mpp) cc_final: 0.6856 (pmm) REVERT: D 996 CYS cc_start: 0.8848 (p) cc_final: 0.8550 (p) outliers start: 4 outliers final: 0 residues processed: 463 average time/residue: 0.1160 time to fit residues: 84.0473 Evaluate side-chains 367 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 1 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 0.0870 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 904 GLN B1006 GLN C 67 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.127343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087470 restraints weight = 61101.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089765 restraints weight = 41688.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091478 restraints weight = 31162.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.092580 restraints weight = 25103.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093466 restraints weight = 21477.847| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17074 Z= 0.151 Angle : 0.636 7.854 23155 Z= 0.337 Chirality : 0.044 0.190 2669 Planarity : 0.005 0.078 3004 Dihedral : 4.925 22.157 2346 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.40 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2181 helix: 0.52 (0.17), residues: 971 sheet: 0.10 (0.40), residues: 173 loop : -2.62 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 933 TYR 0.011 0.001 TYR D 819 PHE 0.022 0.002 PHE D 343 TRP 0.020 0.002 TRP D 511 HIS 0.010 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00334 (17074) covalent geometry : angle 0.63565 (23155) hydrogen bonds : bond 0.03537 ( 696) hydrogen bonds : angle 4.39656 ( 1995) *********************** 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 428 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.657 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: 0.9057 (mmtm) cc_final: 0.8818 (mmtm) REVERT: A 96 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 177 ASN cc_start: 0.9430 (t0) cc_final: 0.9216 (t0) REVERT: A 179 CYS cc_start: 0.8552 (m) cc_final: 0.8337 (m) REVERT: A 199 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 105 GLU cc_start: 0.5647 (pp20) cc_final: 0.5339 (pp20) REVERT: B 140 LEU cc_start: 0.8619 (mm) cc_final: 0.8251 (mm) REVERT: B 248 TRP cc_start: 0.8532 (m100) cc_final: 0.7220 (m100) REVERT: B 257 MET cc_start: 0.8277 (mtm) cc_final: 0.7893 (mtt) REVERT: B 264 VAL cc_start: 0.8811 (t) cc_final: 0.8345 (t) REVERT: B 267 GLU cc_start: 0.8796 (mp0) cc_final: 0.8545 (mp0) REVERT: B 280 VAL cc_start: 0.9448 (t) cc_final: 0.9233 (t) REVERT: B 347 MET cc_start: 0.8832 (ptp) cc_final: 0.8507 (ptt) REVERT: B 406 MET cc_start: 0.8933 (mmp) cc_final: 0.8679 (mmm) REVERT: B 456 HIS cc_start: 0.8756 (p90) cc_final: 0.8100 (p-80) REVERT: B 460 LEU cc_start: 0.9331 (mt) cc_final: 0.9016 (mt) REVERT: B 538 MET cc_start: 0.8950 (ppp) cc_final: 0.8004 (ppp) REVERT: B 933 ARG cc_start: 0.9315 (mpp-170) cc_final: 0.8844 (tpp80) REVERT: B 944 LYS cc_start: 0.9462 (mmpt) cc_final: 0.9137 (mmmt) REVERT: B 979 PHE cc_start: 0.8919 (t80) cc_final: 0.8351 (t80) REVERT: C 136 PHE cc_start: 0.8778 (m-10) cc_final: 0.8386 (t80) REVERT: C 138 LEU cc_start: 0.9028 (mm) cc_final: 0.8602 (mm) REVERT: C 185 GLN cc_start: 0.9001 (mp10) cc_final: 0.8631 (mp10) REVERT: D 122 TYR cc_start: 0.8365 (p90) cc_final: 0.7991 (t80) REVERT: D 202 MET cc_start: 0.8520 (ptp) cc_final: 0.8117 (ptp) REVERT: D 281 PHE cc_start: 0.8325 (m-10) cc_final: 0.8049 (m-10) REVERT: D 308 TYR cc_start: 0.7282 (t80) cc_final: 0.7008 (t80) REVERT: D 382 MET cc_start: 0.7886 (mmp) cc_final: 0.7600 (mmp) REVERT: D 676 ASN cc_start: 0.8990 (t0) cc_final: 0.8633 (t0) REVERT: D 985 MET cc_start: 0.7840 (mpp) cc_final: 0.6948 (pmm) REVERT: D 996 CYS cc_start: 0.8819 (p) cc_final: 0.8495 (p) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.1203 time to fit residues: 79.9586 Evaluate side-chains 352 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.0060 chunk 169 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 GLN B1006 GLN C 67 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089737 restraints weight = 60231.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092253 restraints weight = 40380.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093925 restraints weight = 30118.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095097 restraints weight = 24344.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095938 restraints weight = 20812.641| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17074 Z= 0.118 Angle : 0.635 8.380 23155 Z= 0.332 Chirality : 0.044 0.205 2669 Planarity : 0.004 0.079 3004 Dihedral : 4.837 23.284 2346 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.67 % Favored : 91.10 % Rotamer: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 2181 helix: 0.59 (0.17), residues: 985 sheet: -0.03 (0.40), residues: 184 loop : -2.61 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 933 TYR 0.016 0.001 TYR D 517 PHE 0.020 0.001 PHE A 115 TRP 0.018 0.001 TRP B 266 HIS 0.010 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00266 (17074) covalent geometry : angle 0.63511 (23155) hydrogen bonds : bond 0.03349 ( 696) hydrogen bonds : angle 4.22995 ( 1995) *********************** 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 434 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 0.649 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: 0.9068 (mmtm) cc_final: 0.8840 (mmtm) REVERT: A 96 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 177 ASN cc_start: 0.9445 (t0) cc_final: 0.9230 (t0) REVERT: A 190 GLU cc_start: 0.8176 (pt0) cc_final: 0.7918 (pt0) REVERT: A 199 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 105 GLU cc_start: 0.5637 (pp20) cc_final: 0.5373 (pp20) REVERT: B 140 LEU cc_start: 0.8628 (mm) cc_final: 0.8260 (mm) REVERT: B 146 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8263 (mt-10) REVERT: B 248 TRP cc_start: 0.8541 (m100) cc_final: 0.8045 (m100) REVERT: B 257 MET cc_start: 0.8327 (mtm) cc_final: 0.7984 (mtt) REVERT: B 264 VAL cc_start: 0.8779 (t) cc_final: 0.8285 (t) REVERT: B 267 GLU cc_start: 0.8787 (mp0) cc_final: 0.8492 (mp0) REVERT: B 347 MET cc_start: 0.8835 (ptp) cc_final: 0.8488 (ptt) REVERT: B 406 MET cc_start: 0.8926 (mmp) cc_final: 0.8663 (mmm) REVERT: B 460 LEU cc_start: 0.9373 (mt) cc_final: 0.9065 (mt) REVERT: B 519 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8520 (tm-30) REVERT: B 538 MET cc_start: 0.9018 (ppp) cc_final: 0.8084 (ppp) REVERT: B 560 ASN cc_start: 0.8605 (m110) cc_final: 0.8402 (m110) REVERT: B 933 ARG cc_start: 0.9310 (mpp-170) cc_final: 0.8807 (tpp80) REVERT: B 944 LYS cc_start: 0.9459 (mmpt) cc_final: 0.9137 (mmmt) REVERT: B 979 PHE cc_start: 0.8976 (t80) cc_final: 0.8373 (t80) REVERT: B 995 ARG cc_start: 0.9320 (pmt-80) cc_final: 0.8899 (pmt-80) REVERT: C 110 GLN cc_start: 0.9389 (mp10) cc_final: 0.9129 (mp10) REVERT: C 136 PHE cc_start: 0.8804 (m-10) cc_final: 0.8369 (t80) REVERT: C 138 LEU cc_start: 0.8984 (mm) cc_final: 0.8636 (mm) REVERT: C 185 GLN cc_start: 0.8952 (mp10) cc_final: 0.8512 (mp10) REVERT: D 122 TYR cc_start: 0.8385 (p90) cc_final: 0.7997 (t80) REVERT: D 202 MET cc_start: 0.8514 (ptp) cc_final: 0.8121 (ptp) REVERT: D 212 MET cc_start: -0.0393 (tpt) cc_final: -0.1405 (mmt) REVERT: D 281 PHE cc_start: 0.8231 (m-10) cc_final: 0.7992 (m-10) REVERT: D 308 TYR cc_start: 0.7280 (t80) cc_final: 0.6999 (t80) REVERT: D 512 ILE cc_start: 0.8004 (pt) cc_final: 0.7716 (pt) REVERT: D 520 MET cc_start: 0.8645 (mmm) cc_final: 0.7940 (ptt) REVERT: D 572 ASN cc_start: 0.7226 (m110) cc_final: 0.6953 (p0) REVERT: D 676 ASN cc_start: 0.8998 (t0) cc_final: 0.8450 (t0) REVERT: D 746 ILE cc_start: 0.8549 (pt) cc_final: 0.8157 (mt) REVERT: D 984 LYS cc_start: 0.8351 (ptpt) cc_final: 0.8114 (mmpt) REVERT: D 985 MET cc_start: 0.7771 (mpp) cc_final: 0.6730 (pmm) REVERT: D 996 CYS cc_start: 0.8796 (p) cc_final: 0.8457 (p) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.1226 time to fit residues: 82.0594 Evaluate side-chains 358 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 124 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 22 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 HIS B 519 GLN B 904 GLN B1006 GLN C 67 ASN ** C 96 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.129779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089711 restraints weight = 60189.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091953 restraints weight = 41707.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093451 restraints weight = 31710.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094636 restraints weight = 26143.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095361 restraints weight = 22524.679| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17074 Z= 0.126 Angle : 0.637 9.503 23155 Z= 0.333 Chirality : 0.044 0.169 2669 Planarity : 0.004 0.079 3004 Dihedral : 4.764 21.894 2346 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.12 % Favored : 90.65 % Rotamer: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 2181 helix: 0.64 (0.17), residues: 982 sheet: -0.00 (0.39), residues: 190 loop : -2.58 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 933 TYR 0.011 0.001 TYR B 958 PHE 0.021 0.001 PHE A 166 TRP 0.020 0.002 TRP B 266 HIS 0.010 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00285 (17074) covalent geometry : angle 0.63652 (23155) hydrogen bonds : bond 0.03330 ( 696) hydrogen bonds : angle 4.25542 ( 1995) *********************** 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 430 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.534 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8852 (mmtm) REVERT: A 96 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 177 ASN cc_start: 0.9437 (t0) cc_final: 0.9213 (t0) REVERT: A 190 GLU cc_start: 0.8308 (pt0) cc_final: 0.8032 (pt0) REVERT: A 199 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 105 GLU cc_start: 0.5519 (pp20) cc_final: 0.5257 (pp20) REVERT: B 140 LEU cc_start: 0.8611 (mm) cc_final: 0.8246 (mm) REVERT: B 146 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8230 (mt-10) REVERT: B 248 TRP cc_start: 0.8496 (m100) cc_final: 0.8001 (m100) REVERT: B 264 VAL cc_start: 0.8769 (t) cc_final: 0.8324 (t) REVERT: B 343 PHE cc_start: 0.8740 (t80) cc_final: 0.8452 (t80) REVERT: B 347 MET cc_start: 0.8838 (ptp) cc_final: 0.8208 (ptt) REVERT: B 406 MET cc_start: 0.8946 (mmp) cc_final: 0.8689 (mmm) REVERT: B 456 HIS cc_start: 0.8542 (p90) cc_final: 0.8029 (p-80) REVERT: B 460 LEU cc_start: 0.9355 (mt) cc_final: 0.9058 (mt) REVERT: B 482 THR cc_start: 0.6165 (m) cc_final: 0.5936 (m) REVERT: B 519 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: B 538 MET cc_start: 0.9015 (ppp) cc_final: 0.8032 (ppp) REVERT: B 933 ARG cc_start: 0.9272 (mpp-170) cc_final: 0.8807 (tpp80) REVERT: B 944 LYS cc_start: 0.9445 (mmpt) cc_final: 0.9139 (mmmt) REVERT: B 979 PHE cc_start: 0.8962 (t80) cc_final: 0.8386 (t80) REVERT: B 1007 MET cc_start: 0.9433 (tpt) cc_final: 0.9053 (tpt) REVERT: B 1023 PHE cc_start: 0.9152 (m-80) cc_final: 0.8905 (m-80) REVERT: C 136 PHE cc_start: 0.8807 (m-10) cc_final: 0.8366 (t80) REVERT: C 138 LEU cc_start: 0.9048 (mm) cc_final: 0.8754 (mm) REVERT: C 185 GLN cc_start: 0.9095 (mp10) cc_final: 0.8776 (mp10) REVERT: D 122 TYR cc_start: 0.8386 (p90) cc_final: 0.8003 (t80) REVERT: D 202 MET cc_start: 0.8532 (ptp) cc_final: 0.8149 (ptp) REVERT: D 212 MET cc_start: -0.0190 (tpt) cc_final: -0.1399 (mmt) REVERT: D 281 PHE cc_start: 0.8332 (m-10) cc_final: 0.8051 (m-10) REVERT: D 308 TYR cc_start: 0.7289 (t80) cc_final: 0.6996 (t80) REVERT: D 520 MET cc_start: 0.8661 (mmm) cc_final: 0.7779 (ptt) REVERT: D 538 MET cc_start: 0.6713 (mmp) cc_final: 0.6436 (mmp) REVERT: D 572 ASN cc_start: 0.7224 (m110) cc_final: 0.6924 (p0) REVERT: D 985 MET cc_start: 0.7748 (mpp) cc_final: 0.6993 (pmm) REVERT: D 996 CYS cc_start: 0.8793 (p) cc_final: 0.8500 (p) outliers start: 1 outliers final: 0 residues processed: 429 average time/residue: 0.1228 time to fit residues: 82.0329 Evaluate side-chains 349 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 123 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 15 optimal weight: 0.0040 chunk 166 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 173 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 904 GLN B1006 GLN C 67 ASN ** 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 = 0.3979 r_free = 0.3979 target = 0.130215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089615 restraints weight = 59854.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091947 restraints weight = 41036.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093555 restraints weight = 30869.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094805 restraints weight = 25054.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095702 restraints weight = 21410.636| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17074 Z= 0.119 Angle : 0.639 9.144 23155 Z= 0.334 Chirality : 0.044 0.176 2669 Planarity : 0.005 0.079 3004 Dihedral : 4.725 22.796 2346 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.80 % Favored : 90.97 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 2181 helix: 0.69 (0.17), residues: 982 sheet: 0.03 (0.39), residues: 189 loop : -2.56 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 743 TYR 0.021 0.001 TYR A 108 PHE 0.020 0.001 PHE D 292 TRP 0.029 0.002 TRP B 266 HIS 0.011 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00268 (17074) covalent geometry : angle 0.63928 (23155) hydrogen bonds : bond 0.03249 ( 696) hydrogen bonds : angle 4.17387 ( 1995) *********************** REFINEMENT MACRO_CYCLE 9 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 426 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 0.548 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8854 (mmtm) REVERT: A 96 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 177 ASN cc_start: 0.9413 (t0) cc_final: 0.9206 (t0) REVERT: A 179 CYS cc_start: 0.8443 (m) cc_final: 0.8204 (m) REVERT: A 199 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 105 GLU cc_start: 0.5637 (pp20) cc_final: 0.5427 (pp20) REVERT: B 140 LEU cc_start: 0.8672 (mm) cc_final: 0.8328 (mm) REVERT: B 248 TRP cc_start: 0.8548 (m100) cc_final: 0.8042 (m100) REVERT: B 264 VAL cc_start: 0.8853 (t) cc_final: 0.8483 (t) REVERT: B 343 PHE cc_start: 0.8712 (t80) cc_final: 0.8413 (t80) REVERT: B 347 MET cc_start: 0.8817 (ptp) cc_final: 0.8190 (ptt) REVERT: B 406 MET cc_start: 0.9011 (mmp) cc_final: 0.8768 (mmm) REVERT: B 456 HIS cc_start: 0.9004 (p90) cc_final: 0.8443 (p-80) REVERT: B 460 LEU cc_start: 0.9362 (mt) cc_final: 0.9057 (mt) REVERT: B 482 THR cc_start: 0.6095 (m) cc_final: 0.5879 (m) REVERT: B 538 MET cc_start: 0.9052 (ppp) cc_final: 0.8052 (ppp) REVERT: B 933 ARG cc_start: 0.9315 (mpp-170) cc_final: 0.8833 (tpp80) REVERT: B 944 LYS cc_start: 0.9443 (mmpt) cc_final: 0.9149 (mmmt) REVERT: B 979 PHE cc_start: 0.9004 (t80) cc_final: 0.8419 (t80) REVERT: B 988 VAL cc_start: 0.8691 (t) cc_final: 0.8399 (p) REVERT: B 1003 LEU cc_start: 0.9813 (tp) cc_final: 0.9592 (tp) REVERT: B 1007 MET cc_start: 0.9424 (tpt) cc_final: 0.9065 (tpt) REVERT: B 1023 PHE cc_start: 0.9059 (m-80) cc_final: 0.8767 (m-80) REVERT: C 136 PHE cc_start: 0.8811 (m-10) cc_final: 0.8300 (t80) REVERT: C 138 LEU cc_start: 0.9007 (mm) cc_final: 0.8747 (mm) REVERT: C 185 GLN cc_start: 0.9089 (mp10) cc_final: 0.8768 (mp10) REVERT: D 122 TYR cc_start: 0.8381 (p90) cc_final: 0.8013 (t80) REVERT: D 202 MET cc_start: 0.8493 (ptp) cc_final: 0.8076 (ptp) REVERT: D 212 MET cc_start: -0.0313 (tpt) cc_final: -0.1460 (mmt) REVERT: D 281 PHE cc_start: 0.8315 (m-10) cc_final: 0.8038 (m-10) REVERT: D 299 LEU cc_start: 0.7986 (mt) cc_final: 0.7718 (mt) REVERT: D 308 TYR cc_start: 0.7315 (t80) cc_final: 0.7047 (t80) REVERT: D 520 MET cc_start: 0.8662 (mmm) cc_final: 0.7815 (ptt) REVERT: D 676 ASN cc_start: 0.9077 (t0) cc_final: 0.8682 (t0) REVERT: D 984 LYS cc_start: 0.8389 (ptpt) cc_final: 0.8136 (mmpt) REVERT: D 985 MET cc_start: 0.7780 (mpp) cc_final: 0.6812 (pmm) REVERT: D 996 CYS cc_start: 0.8746 (p) cc_final: 0.8394 (p) outliers start: 1 outliers final: 0 residues processed: 425 average time/residue: 0.1200 time to fit residues: 79.5730 Evaluate side-chains 358 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 91 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 904 GLN B1006 GLN C 67 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090501 restraints weight = 58664.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092847 restraints weight = 40373.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094505 restraints weight = 30352.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095626 restraints weight = 24759.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096423 restraints weight = 21202.882| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17074 Z= 0.116 Angle : 0.646 9.963 23155 Z= 0.333 Chirality : 0.044 0.184 2669 Planarity : 0.004 0.079 3004 Dihedral : 4.633 21.676 2346 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.80 % Favored : 90.97 % Rotamer: Outliers : 0.06 % Allowed : 0.58 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.18), residues: 2181 helix: 0.73 (0.17), residues: 967 sheet: 0.09 (0.39), residues: 190 loop : -2.52 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 743 TYR 0.014 0.001 TYR A 108 PHE 0.021 0.001 PHE D 292 TRP 0.028 0.002 TRP D 511 HIS 0.008 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00264 (17074) covalent geometry : angle 0.64588 (23155) hydrogen bonds : bond 0.03219 ( 696) hydrogen bonds : angle 4.15106 ( 1995) ********************** REFINEMENT MACRO_CYCLE 10 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 434 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 0.617 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: symmetry clash REVERT: A 71 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8876 (mmtm) REVERT: A 96 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 199 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 105 GLU cc_start: 0.5943 (pp20) cc_final: 0.5710 (pp20) REVERT: B 140 LEU cc_start: 0.8669 (mm) cc_final: 0.8169 (mm) REVERT: B 248 TRP cc_start: 0.8544 (m100) cc_final: 0.8071 (m100) REVERT: B 264 VAL cc_start: 0.8834 (t) cc_final: 0.8551 (t) REVERT: B 347 MET cc_start: 0.8800 (ptp) cc_final: 0.8470 (ptt) REVERT: B 398 ASP cc_start: 0.8920 (m-30) cc_final: 0.8160 (m-30) REVERT: B 406 MET cc_start: 0.9036 (mmp) cc_final: 0.8780 (mmm) REVERT: B 456 HIS cc_start: 0.9012 (p90) cc_final: 0.8462 (p-80) REVERT: B 460 LEU cc_start: 0.9352 (mt) cc_final: 0.9056 (mt) REVERT: B 482 THR cc_start: 0.6028 (m) cc_final: 0.5812 (m) REVERT: B 538 MET cc_start: 0.9028 (ppp) cc_final: 0.8086 (ppp) REVERT: B 567 TYR cc_start: 0.9394 (m-10) cc_final: 0.9117 (m-10) REVERT: B 933 ARG cc_start: 0.9257 (mpp-170) cc_final: 0.8832 (tpp-160) REVERT: B 944 LYS cc_start: 0.9430 (mmpt) cc_final: 0.9121 (mmmt) REVERT: B 979 PHE cc_start: 0.8992 (t80) cc_final: 0.8390 (t80) REVERT: B 988 VAL cc_start: 0.8688 (t) cc_final: 0.8438 (p) REVERT: B 1003 LEU cc_start: 0.9803 (tp) cc_final: 0.9589 (tp) REVERT: B 1007 MET cc_start: 0.9446 (tpt) cc_final: 0.9100 (tpt) REVERT: B 1023 PHE cc_start: 0.9076 (m-80) cc_final: 0.8804 (m-80) REVERT: C 104 ILE cc_start: 0.8897 (mm) cc_final: 0.8161 (tp) REVERT: C 111 GLU cc_start: 0.9249 (pm20) cc_final: 0.8802 (pm20) REVERT: C 136 PHE cc_start: 0.8793 (m-10) cc_final: 0.8252 (t80) REVERT: C 138 LEU cc_start: 0.8994 (mm) cc_final: 0.8737 (mm) REVERT: C 185 GLN cc_start: 0.9160 (mp10) cc_final: 0.8668 (mp10) REVERT: D 122 TYR cc_start: 0.8375 (p90) cc_final: 0.8018 (t80) REVERT: D 202 MET cc_start: 0.8574 (ptp) cc_final: 0.8212 (ptp) REVERT: D 212 MET cc_start: -0.0411 (tpt) cc_final: -0.1497 (mmt) REVERT: D 281 PHE cc_start: 0.8333 (m-10) cc_final: 0.8056 (m-10) REVERT: D 308 TYR cc_start: 0.7325 (t80) cc_final: 0.7065 (t80) REVERT: D 612 TYR cc_start: 0.8835 (t80) cc_final: 0.8565 (t80) REVERT: D 676 ASN cc_start: 0.9010 (t0) cc_final: 0.8650 (t0) REVERT: D 783 MET cc_start: 0.8568 (mpp) cc_final: 0.7894 (mpp) REVERT: D 985 MET cc_start: 0.7870 (mpp) cc_final: 0.7063 (pmm) REVERT: D 996 CYS cc_start: 0.8725 (p) cc_final: 0.8378 (p) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.1148 time to fit residues: 76.9525 Evaluate side-chains 349 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 166 optimal weight: 0.0060 chunk 185 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 904 GLN B1006 GLN C 67 ASN ** 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 = 0.3979 r_free = 0.3979 target = 0.129702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089386 restraints weight = 60778.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091761 restraints weight = 40806.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093443 restraints weight = 30626.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094493 restraints weight = 24716.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.095388 restraints weight = 21395.268| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17074 Z= 0.127 Angle : 0.659 10.571 23155 Z= 0.343 Chirality : 0.045 0.200 2669 Planarity : 0.005 0.079 3004 Dihedral : 4.641 22.001 2346 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.99 % Favored : 90.78 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 2181 helix: 0.74 (0.17), residues: 976 sheet: 0.08 (0.39), residues: 189 loop : -2.51 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 933 TYR 0.021 0.001 TYR D 237 PHE 0.020 0.001 PHE D 292 TRP 0.027 0.002 TRP B 266 HIS 0.011 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00290 (17074) covalent geometry : angle 0.65863 (23155) hydrogen bonds : bond 0.03299 ( 696) hydrogen bonds : angle 4.16456 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3531.02 seconds wall clock time: 61 minutes 30.31 seconds (3690.31 seconds total)