Starting phenix.real_space_refine on Sun Aug 24 19:26:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h93_34552/08_2025/8h93_34552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h93_34552/08_2025/8h93_34552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h93_34552/08_2025/8h93_34552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h93_34552/08_2025/8h93_34552.map" model { file = "/net/cci-nas-00/data/ceres_data/8h93_34552/08_2025/8h93_34552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h93_34552/08_2025/8h93_34552.cif" } resolution = 3.01 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= 0.046 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 181 5.16 5 C 14111 2.51 5 N 3795 2.21 5 O 4104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7481 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "D" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7476 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Time building chain proxies: 5.62, per 1000 atoms: 0.25 Number of scatterers: 22191 At special positions: 0 Unit cell: (101.2, 101.2, 226.6, 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 181 16.00 O 4104 8.00 N 3795 7.00 C 14111 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: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 23 sheets defined 41.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.508A pdb=" N VAL A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.759A pdb=" N SER A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 292 through 304 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.874A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 Processing helix chain 'A' and resid 329 through 346 removed outlier: 3.614A pdb=" N LYS A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 373 Processing helix chain 'A' and resid 380 through 401 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.746A pdb=" N LEU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 444 through 462 removed outlier: 3.660A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY A 460 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.892A pdb=" N GLY A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.730A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 4.025A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.502A pdb=" N VAL A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.917A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 removed outlier: 3.709A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 695 removed outlier: 3.748A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.531A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'A' and resid 852 through 865 removed outlier: 3.818A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 removed outlier: 3.615A pdb=" N GLU A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 937 through 950 removed outlier: 3.912A pdb=" N GLN A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 978 removed outlier: 4.433A pdb=" N ALA A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1007 Processing helix chain 'A' and resid 1018 through 1022 Processing helix chain 'A' and resid 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.581A pdb=" N ALA A1048 " --> pdb=" O ASP A1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 removed outlier: 3.533A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.853A pdb=" N VAL C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 42' Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.859A pdb=" N GLY C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 94 through 114 removed outlier: 3.531A pdb=" N GLU C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.691A pdb=" N LYS D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.618A pdb=" N ALA D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 198 removed outlier: 4.063A pdb=" N GLU D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 211 removed outlier: 3.789A pdb=" N THR D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 4.097A pdb=" N SER D 227 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.628A pdb=" N LEU D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 280 removed outlier: 4.426A pdb=" N LEU D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 3.521A pdb=" N ASN D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.718A pdb=" N ASN D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.040A pdb=" N PHE D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 346 Processing helix chain 'D' and resid 356 through 373 removed outlier: 3.603A pdb=" N LYS D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 444 through 459 removed outlier: 4.170A pdb=" N TYR D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 462 No H-bonds generated for 'chain 'D' and resid 460 through 462' Processing helix chain 'D' and resid 488 through 498 Processing helix chain 'D' and resid 500 through 512 removed outlier: 3.692A pdb=" N LEU D 510 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 532 removed outlier: 3.613A pdb=" N LYS D 522 " --> pdb=" O THR D 518 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 552 removed outlier: 3.572A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 574 through 586 removed outlier: 4.185A pdb=" N LYS D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 639 Processing helix chain 'D' and resid 653 through 665 removed outlier: 3.576A pdb=" N LEU D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 695 removed outlier: 3.736A pdb=" N LEU D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 693 " --> pdb=" O TRP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 722 removed outlier: 3.627A pdb=" N MET D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 751 removed outlier: 3.913A pdb=" N MET D 744 " --> pdb=" O ILE D 740 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 745 " --> pdb=" O GLY D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 779 Processing helix chain 'D' and resid 795 through 807 removed outlier: 3.589A pdb=" N LEU D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 802 " --> pdb=" O SER D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 836 removed outlier: 3.562A pdb=" N VAL D 827 " --> pdb=" O GLY D 823 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN D 836 " --> pdb=" O GLN D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 865 removed outlier: 3.929A pdb=" N GLY D 857 " --> pdb=" O ASP D 853 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 865 " --> pdb=" O MET D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 892 Processing helix chain 'D' and resid 910 through 923 removed outlier: 4.192A pdb=" N GLU D 914 " --> pdb=" O GLN D 910 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 921 " --> pdb=" O ALA D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 951 removed outlier: 3.736A pdb=" N GLY D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 947 " --> pdb=" O THR D 943 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 951 " --> pdb=" O GLY D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 979 removed outlier: 3.543A pdb=" N CYS D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1006 Processing helix chain 'D' and resid 1018 through 1022 removed outlier: 3.699A pdb=" N TYR D1022 " --> pdb=" O LYS D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1023 through 1037 removed outlier: 3.520A pdb=" N GLU D1034 " --> pdb=" O LEU D1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 174 removed outlier: 3.566A pdb=" N LEU E 162 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 163 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 174 " --> pdb=" O PHE E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'F' and resid 37 through 42 removed outlier: 3.697A pdb=" N VAL F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER F 42 " --> pdb=" O ILE F 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 37 through 42' Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.716A pdb=" N ARG F 56 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 73 Processing helix chain 'F' and resid 94 through 114 removed outlier: 3.563A pdb=" N ARG F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178 removed outlier: 6.755A pdb=" N ILE A 175 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP A 220 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 177 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 217 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR A 267 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 219 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ARG A 269 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 145 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS A 144 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 432 removed outlier: 4.124A pdb=" N CYS A 439 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 571 removed outlier: 3.503A pdb=" N ILE A 594 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 675 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY A 704 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 731 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 759 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 732 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 761 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 790 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 847 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 873 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 875 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 961 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 989 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 removed outlier: 8.519A pdb=" N ASP B 328 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 289 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 576 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 289 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 574 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 296 through 300 removed outlier: 4.360A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 351 removed outlier: 3.526A pdb=" N ALA B 360 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 369 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 396 removed outlier: 3.598A pdb=" N TRP B 414 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 404 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 412 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 423 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP B 415 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 421 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.872A pdb=" N GLY B 445 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU B 451 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 464 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 453 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 455 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 460 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 475 removed outlier: 6.524A pdb=" N GLY B 486 " --> pdb=" O MET B 472 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 474 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 484 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS B 492 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 518 removed outlier: 3.521A pdb=" N LYS B 517 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.836A pdb=" N GLU C 88 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 79 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.709A pdb=" N PHE D 177 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 145 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR D 285 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 567 through 571 Processing sheet with id=AB6, first strand: chain 'D' and resid 644 through 645 removed outlier: 3.657A pdb=" N LEU D 674 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 702 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA D 761 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 788 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS D 816 " --> pdb=" O LEU D 787 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 873 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 872 " --> pdb=" O GLU D 900 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU D 901 " --> pdb=" O ASP D 930 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 961 " --> pdb=" O LEU D 931 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL D 989 " --> pdb=" O LEU D 960 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 327 through 328 removed outlier: 8.623A pdb=" N ASP E 328 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL E 289 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU E 284 " --> pdb=" O LYS E 580 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS E 580 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS E 286 " --> pdb=" O HIS E 578 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS E 578 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 288 " --> pdb=" O VAL E 576 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 307 through 312 removed outlier: 3.651A pdb=" N VAL E 318 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 333 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 346 through 351 removed outlier: 3.845A pdb=" N THR E 348 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 358 " --> pdb=" O TRP E 371 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 370 " --> pdb=" O LYS E 381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 395 through 396 removed outlier: 3.545A pdb=" N ALA E 404 " --> pdb=" O ARG E 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 412 " --> pdb=" O ALA E 404 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL E 411 " --> pdb=" O ASN E 424 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN E 424 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE E 413 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 420 " --> pdb=" O ASP E 415 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 436 through 437 removed outlier: 3.868A pdb=" N ARG E 452 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 451 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 464 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS E 453 " --> pdb=" O SER E 462 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP E 455 " --> pdb=" O LYS E 460 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS E 460 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 471 through 476 removed outlier: 6.284A pdb=" N GLY E 486 " --> pdb=" O MET E 472 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU E 474 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 484 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N HIS E 476 " --> pdb=" O TRP E 482 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TRP E 482 " --> pdb=" O HIS E 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS E 493 " --> pdb=" O LEU E 485 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP E 507 " --> pdb=" O HIS E 492 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU E 494 " --> pdb=" O THR E 505 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR E 505 " --> pdb=" O LEU E 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 515 through 518 removed outlier: 3.755A pdb=" N LYS E 517 " --> pdb=" O ALA E 526 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 534 " --> pdb=" O GLN E 547 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN E 547 " --> pdb=" O ILE E 534 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL E 536 " --> pdb=" O LEU E 545 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 47 through 50 removed outlier: 3.963A pdb=" N GLU F 88 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2688 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: 4.74 Time building geometry restraints manager: 2.42 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: 5118 1.33 - 1.45: 4619 1.45 - 1.58: 12629 1.58 - 1.70: 0 1.70 - 1.83: 255 Bond restraints: 22621 Sorted by residual: bond pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.06e+01 bond pdb=" N VAL C 46 " pdb=" CA VAL C 46 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.45e+00 bond pdb=" N VAL F 46 " pdb=" CA VAL F 46 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.05e+00 bond pdb=" N ILE F 38 " pdb=" CA ILE F 38 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.67e+00 bond pdb=" N VAL C 41 " pdb=" CA VAL C 41 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.33e+00 ... (remaining 22616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 30017 2.20 - 4.41: 536 4.41 - 6.61: 64 6.61 - 8.81: 18 8.81 - 11.01: 4 Bond angle restraints: 30639 Sorted by residual: angle pdb=" N PRO F 44 " pdb=" CA PRO F 44 " pdb=" C PRO F 44 " ideal model delta sigma weight residual 113.40 124.41 -11.01 1.34e+00 5.57e-01 6.76e+01 angle pdb=" C PRO C 44 " pdb=" CA PRO C 44 " pdb=" CB PRO C 44 " ideal model delta sigma weight residual 111.23 103.08 8.15 1.28e+00 6.10e-01 4.05e+01 angle pdb=" C ALA D 561 " pdb=" N LEU D 562 " pdb=" CA LEU D 562 " ideal model delta sigma weight residual 123.05 115.82 7.23 1.40e+00 5.10e-01 2.67e+01 angle pdb=" C PRO F 44 " pdb=" CA PRO F 44 " pdb=" CB PRO F 44 " ideal model delta sigma weight residual 112.55 105.58 6.97 1.50e+00 4.44e-01 2.16e+01 angle pdb=" CA SER F 42 " pdb=" C SER F 42 " pdb=" O SER F 42 " ideal model delta sigma weight residual 120.55 116.06 4.49 1.06e+00 8.90e-01 1.79e+01 ... (remaining 30634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11928 17.97 - 35.94: 1363 35.94 - 53.91: 306 53.91 - 71.88: 57 71.88 - 89.84: 39 Dihedral angle restraints: 13693 sinusoidal: 5495 harmonic: 8198 Sorted by residual: dihedral pdb=" CD ARG C 32 " pdb=" NE ARG C 32 " pdb=" CZ ARG C 32 " pdb=" NH1 ARG C 32 " ideal model delta sinusoidal sigma weight residual 0.00 -73.21 73.21 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CD ARG D 564 " pdb=" NE ARG D 564 " pdb=" CZ ARG D 564 " pdb=" NH1 ARG D 564 " ideal model delta sinusoidal sigma weight residual 0.00 47.97 -47.97 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CA LYS D 170 " pdb=" C LYS D 170 " pdb=" N MET D 171 " pdb=" CA MET D 171 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 13690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2899 0.052 - 0.104: 485 0.104 - 0.156: 122 0.156 - 0.208: 18 0.208 - 0.260: 4 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA ILE A 771 " pdb=" N ILE A 771 " pdb=" C ILE A 771 " pdb=" CB ILE A 771 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU C 45 " pdb=" N LEU C 45 " pdb=" C LEU C 45 " pdb=" CB LEU C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PRO F 44 " pdb=" N PRO F 44 " pdb=" C PRO F 44 " pdb=" CB PRO F 44 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3525 not shown) Planarity restraints: 3878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 32 " -1.054 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG C 32 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 32 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 32 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 32 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 564 " -0.815 9.50e-02 1.11e+02 3.65e-01 8.11e+01 pdb=" NE ARG D 564 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG D 564 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 564 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 564 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 452 " 0.672 9.50e-02 1.11e+02 3.01e-01 5.54e+01 pdb=" NE ARG B 452 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG B 452 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 452 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 452 " 0.021 2.00e-02 2.50e+03 ... (remaining 3875 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 488 2.69 - 3.25: 22354 3.25 - 3.80: 34553 3.80 - 4.35: 44642 4.35 - 4.90: 72405 Nonbonded interactions: 174442 Sorted by model distance: nonbonded pdb=" OE2 GLU B 550 " pdb=" OH TYR B 577 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR D 966 " pdb=" OD1 ASN D 968 " model vdw 2.195 3.040 nonbonded pdb=" O LYS D 690 " pdb=" OG SER D 694 " model vdw 2.201 3.040 nonbonded pdb=" O ALA A 864 " pdb=" OG1 THR A 895 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR D 856 " pdb=" O PRO D 878 " model vdw 2.214 3.040 ... (remaining 174437 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 97 through 723 or (resid 724 through 725 and (name N or na \ me CA or name C or name O or name CB )) or resid 726 through 1059)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.530 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 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 0.053 22621 Z= 0.214 Angle : 0.679 11.015 30639 Z= 0.400 Chirality : 0.044 0.260 3528 Planarity : 0.012 0.472 3878 Dihedral : 16.454 89.845 8349 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.08 % Allowed : 14.73 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2790 helix: 1.82 (0.16), residues: 1029 sheet: -0.09 (0.22), residues: 578 loop : -1.32 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 100 TYR 0.014 0.001 TYR D1023 PHE 0.025 0.001 PHE D 177 TRP 0.035 0.001 TRP A 629 HIS 0.008 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00342 (22621) covalent geometry : angle 0.67921 (30639) hydrogen bonds : bond 0.25796 ( 925) hydrogen bonds : angle 7.32448 ( 2688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.7183 (p90) cc_final: 0.6896 (p90) REVERT: A 225 MET cc_start: 0.5194 (mmt) cc_final: 0.4690 (mmp) REVERT: A 279 MET cc_start: 0.5437 (pmm) cc_final: 0.4880 (mtm) REVERT: A 699 LYS cc_start: 0.7447 (mppt) cc_final: 0.6865 (mppt) REVERT: A 754 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6893 (mpt180) REVERT: A 854 ASP cc_start: 0.7006 (t70) cc_final: 0.6627 (t0) REVERT: A 964 LYS cc_start: 0.7513 (tmmt) cc_final: 0.7185 (tmmt) REVERT: B 359 PHE cc_start: 0.7285 (m-80) cc_final: 0.7025 (m-10) REVERT: B 451 LEU cc_start: 0.6753 (mp) cc_final: 0.6303 (mp) REVERT: B 458 MET cc_start: 0.5754 (ppp) cc_final: 0.5512 (mmt) REVERT: B 474 LEU cc_start: 0.8337 (mm) cc_final: 0.8062 (mp) REVERT: D 122 MET cc_start: 0.4659 (tpt) cc_final: 0.4285 (mmt) REVERT: D 137 GLN cc_start: 0.6639 (tm-30) cc_final: 0.6345 (tm-30) REVERT: D 366 PHE cc_start: 0.5931 (m-10) cc_final: 0.5698 (m-80) REVERT: D 401 MET cc_start: 0.4337 (mtt) cc_final: 0.4096 (mtm) REVERT: D 440 TYR cc_start: 0.7853 (m-80) cc_final: 0.7524 (m-80) REVERT: D 487 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.7106 (ptp-170) REVERT: D 565 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: D 622 LYS cc_start: 0.5693 (tppt) cc_final: 0.5205 (tttt) REVERT: D 657 MET cc_start: 0.7341 (tpt) cc_final: 0.6899 (tpt) REVERT: D 668 SER cc_start: 0.7795 (t) cc_final: 0.7457 (t) REVERT: D 744 MET cc_start: 0.7652 (mpp) cc_final: 0.7266 (mtm) REVERT: D 854 ASP cc_start: 0.7400 (p0) cc_final: 0.6888 (t0) REVERT: D 919 MET cc_start: 0.6217 (tmm) cc_final: 0.5656 (tmm) REVERT: D 1021 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5614 (mt-10) REVERT: E 401 MET cc_start: 0.4286 (pmm) cc_final: 0.3971 (pmm) REVERT: E 439 ASP cc_start: 0.7556 (p0) cc_final: 0.6996 (p0) REVERT: E 493 CYS cc_start: 0.7665 (m) cc_final: 0.7222 (t) REVERT: F 108 MET cc_start: 0.7557 (mmp) cc_final: 0.6627 (ttm) outliers start: 27 outliers final: 9 residues processed: 334 average time/residue: 0.1674 time to fit residues: 86.8470 Evaluate side-chains 236 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 298 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 427 ASN A 467 HIS ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 156 GLN B 177 ASN B 285 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 ASN D 566 GLN D 574 GLN D 848 HIS D1011 ASN E 578 HIS F 112 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.187808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.150902 restraints weight = 38633.833| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.16 r_work: 0.4263 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22621 Z= 0.123 Angle : 0.627 11.964 30639 Z= 0.316 Chirality : 0.041 0.175 3528 Planarity : 0.004 0.098 3878 Dihedral : 5.235 88.447 2991 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.28 % Allowed : 15.13 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2790 helix: 1.79 (0.15), residues: 1078 sheet: 0.07 (0.23), residues: 563 loop : -1.51 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.018 0.002 TYR A 247 PHE 0.017 0.001 PHE E 557 TRP 0.014 0.001 TRP E 525 HIS 0.019 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00257 (22621) covalent geometry : angle 0.62662 (30639) hydrogen bonds : bond 0.04808 ( 925) hydrogen bonds : angle 5.07412 ( 2688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8459 (tp40) cc_final: 0.7704 (pm20) REVERT: A 289 GLU cc_start: 0.4971 (pm20) cc_final: 0.4746 (pm20) REVERT: A 770 MET cc_start: 0.7496 (ttm) cc_final: 0.7174 (ttm) REVERT: A 973 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6984 (tt) REVERT: B 171 MET cc_start: 0.6971 (tpp) cc_final: 0.5542 (tmm) REVERT: B 277 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7609 (mmp-170) REVERT: B 295 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.4022 (tp) REVERT: B 458 MET cc_start: 0.6432 (ppp) cc_final: 0.5787 (mmt) REVERT: B 474 LEU cc_start: 0.8610 (mm) cc_final: 0.8148 (mt) REVERT: D 122 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5110 (mmt) REVERT: D 137 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6490 (tm-30) REVERT: D 251 TYR cc_start: 0.6409 (t80) cc_final: 0.6006 (t80) REVERT: D 273 LEU cc_start: 0.7648 (tp) cc_final: 0.7080 (tt) REVERT: D 401 MET cc_start: 0.4930 (mtt) cc_final: 0.4638 (mtm) REVERT: D 487 ARG cc_start: 0.7470 (ptp-170) cc_final: 0.7235 (ptp-170) REVERT: D 553 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6729 (mm-40) REVERT: D 565 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: D 622 LYS cc_start: 0.6038 (tppt) cc_final: 0.5605 (tttp) REVERT: D 657 MET cc_start: 0.8111 (tpt) cc_final: 0.7893 (tpt) REVERT: D 668 SER cc_start: 0.7879 (t) cc_final: 0.7656 (t) REVERT: D 744 MET cc_start: 0.7741 (mpp) cc_final: 0.7161 (mtt) REVERT: D 781 MET cc_start: 0.6441 (ppp) cc_final: 0.6101 (ppp) REVERT: D 854 ASP cc_start: 0.7013 (p0) cc_final: 0.6643 (t0) REVERT: D 919 MET cc_start: 0.7430 (tmm) cc_final: 0.7076 (tmm) REVERT: D 1021 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5642 (mt-10) REVERT: E 171 MET cc_start: 0.6725 (ppp) cc_final: 0.6522 (ppp) REVERT: E 439 ASP cc_start: 0.7190 (p0) cc_final: 0.6546 (p0) REVERT: E 493 CYS cc_start: 0.7339 (m) cc_final: 0.7029 (t) REVERT: F 49 MET cc_start: 0.6418 (mmm) cc_final: 0.6168 (mpp) REVERT: F 108 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6503 (ttm) outliers start: 57 outliers final: 23 residues processed: 294 average time/residue: 0.1497 time to fit residues: 71.5315 Evaluate side-chains 247 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 20 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 323 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN E 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.180127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.142787 restraints weight = 39248.173| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 3.06 r_work: 0.4156 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22621 Z= 0.203 Angle : 0.695 11.121 30639 Z= 0.352 Chirality : 0.044 0.205 3528 Planarity : 0.004 0.049 3878 Dihedral : 5.371 75.192 2978 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.88 % Allowed : 17.57 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 2790 helix: 1.47 (0.15), residues: 1075 sheet: -0.24 (0.22), residues: 570 loop : -1.71 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 146 TYR 0.021 0.002 TYR D 440 PHE 0.029 0.002 PHE D 366 TRP 0.019 0.002 TRP E 525 HIS 0.015 0.002 HIS E 292 Details of bonding type rmsd covalent geometry : bond 0.00460 (22621) covalent geometry : angle 0.69456 (30639) hydrogen bonds : bond 0.05724 ( 925) hydrogen bonds : angle 5.12189 ( 2688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 223 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.6571 (t80) cc_final: 0.6294 (t80) REVERT: A 393 MET cc_start: 0.8428 (ptp) cc_final: 0.8042 (ptm) REVERT: A 708 MET cc_start: 0.7477 (tpt) cc_final: 0.7192 (tpt) REVERT: A 770 MET cc_start: 0.7655 (ttm) cc_final: 0.7307 (ttm) REVERT: A 884 MET cc_start: 0.7762 (tpt) cc_final: 0.7424 (tpp) REVERT: A 973 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6950 (tt) REVERT: B 443 TRP cc_start: 0.6712 (m100) cc_final: 0.5855 (m100) REVERT: B 472 MET cc_start: 0.7245 (mpp) cc_final: 0.6715 (mpp) REVERT: B 474 LEU cc_start: 0.8581 (mm) cc_final: 0.8209 (mt) REVERT: D 122 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5053 (mmt) REVERT: D 171 MET cc_start: 0.4274 (mtt) cc_final: 0.3925 (mtt) REVERT: D 216 LEU cc_start: 0.8022 (tp) cc_final: 0.7810 (tp) REVERT: D 401 MET cc_start: 0.5093 (mtt) cc_final: 0.4825 (mtm) REVERT: D 487 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7313 (ptp-170) REVERT: D 544 ASP cc_start: 0.8208 (t0) cc_final: 0.7957 (t0) REVERT: D 565 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: D 668 SER cc_start: 0.8013 (t) cc_final: 0.7640 (p) REVERT: D 680 GLU cc_start: 0.4127 (mp0) cc_final: 0.2858 (tt0) REVERT: D 744 MET cc_start: 0.7681 (mpp) cc_final: 0.7114 (mpp) REVERT: D 781 MET cc_start: 0.6415 (ppp) cc_final: 0.6054 (ppp) REVERT: D 854 ASP cc_start: 0.7174 (p0) cc_final: 0.6683 (t0) REVERT: D 1021 GLU cc_start: 0.6573 (mm-30) cc_final: 0.5754 (mt-10) REVERT: E 567 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7378 (mm) REVERT: F 49 MET cc_start: 0.7098 (mmm) cc_final: 0.6808 (mmt) REVERT: F 108 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6464 (ttm) outliers start: 97 outliers final: 52 residues processed: 297 average time/residue: 0.1369 time to fit residues: 67.9407 Evaluate side-chains 269 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 470 PHE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 138 optimal weight: 20.0000 chunk 241 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 266 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 160 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.182628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.145630 restraints weight = 38928.755| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.06 r_work: 0.4205 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22621 Z= 0.123 Angle : 0.604 12.793 30639 Z= 0.302 Chirality : 0.041 0.192 3528 Planarity : 0.004 0.044 3878 Dihedral : 5.098 73.204 2978 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.20 % Allowed : 19.46 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2790 helix: 1.59 (0.15), residues: 1077 sheet: -0.22 (0.22), residues: 559 loop : -1.72 (0.16), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.015 0.001 TYR A 247 PHE 0.016 0.001 PHE E 557 TRP 0.019 0.001 TRP E 525 HIS 0.011 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00269 (22621) covalent geometry : angle 0.60444 (30639) hydrogen bonds : bond 0.04370 ( 925) hydrogen bonds : angle 4.77519 ( 2688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6362 (tt) REVERT: A 770 MET cc_start: 0.7624 (ttm) cc_final: 0.7278 (ttm) REVERT: A 884 MET cc_start: 0.7758 (tpt) cc_final: 0.7413 (tpp) REVERT: B 323 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.7013 (p0) REVERT: B 443 TRP cc_start: 0.6676 (m100) cc_final: 0.5862 (m100) REVERT: B 458 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6499 (ptp) REVERT: B 472 MET cc_start: 0.7091 (mpp) cc_final: 0.6445 (mpp) REVERT: B 474 LEU cc_start: 0.8674 (mm) cc_final: 0.8306 (mt) REVERT: D 122 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5155 (mmt) REVERT: D 171 MET cc_start: 0.4398 (mtt) cc_final: 0.4117 (mtt) REVERT: D 401 MET cc_start: 0.5119 (mtt) cc_final: 0.4837 (mtm) REVERT: D 425 HIS cc_start: 0.8021 (m170) cc_final: 0.7769 (m170) REVERT: D 487 ARG cc_start: 0.7608 (ptp-170) cc_final: 0.7276 (ptp-170) REVERT: D 544 ASP cc_start: 0.8153 (t0) cc_final: 0.7889 (t0) REVERT: D 565 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: D 668 SER cc_start: 0.8019 (t) cc_final: 0.7687 (p) REVERT: D 770 MET cc_start: 0.8437 (tpp) cc_final: 0.8105 (tpt) REVERT: D 781 MET cc_start: 0.6335 (ppp) cc_final: 0.5979 (ppp) REVERT: D 854 ASP cc_start: 0.7068 (p0) cc_final: 0.6622 (t0) REVERT: E 171 MET cc_start: 0.7096 (ppp) cc_final: 0.6886 (ppp) REVERT: E 416 LEU cc_start: 0.6905 (tp) cc_final: 0.6626 (mm) REVERT: E 439 ASP cc_start: 0.7093 (p0) cc_final: 0.6459 (p0) REVERT: E 491 GLN cc_start: 0.6225 (tt0) cc_final: 0.5687 (tm-30) REVERT: F 108 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6425 (ttm) outliers start: 80 outliers final: 49 residues processed: 287 average time/residue: 0.1440 time to fit residues: 68.5024 Evaluate side-chains 265 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 210 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 18 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 122 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 269 optimal weight: 0.0970 chunk 94 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 574 GLN B 148 GLN B 323 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.182339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.145420 restraints weight = 38922.343| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.05 r_work: 0.4202 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22621 Z= 0.124 Angle : 0.601 12.908 30639 Z= 0.300 Chirality : 0.041 0.200 3528 Planarity : 0.004 0.045 3878 Dihedral : 4.996 69.419 2978 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.00 % Allowed : 19.94 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2790 helix: 1.60 (0.15), residues: 1077 sheet: -0.26 (0.22), residues: 563 loop : -1.72 (0.16), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.014 0.001 TYR D 856 PHE 0.015 0.001 PHE E 557 TRP 0.019 0.001 TRP E 525 HIS 0.014 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00273 (22621) covalent geometry : angle 0.60113 (30639) hydrogen bonds : bond 0.04204 ( 925) hydrogen bonds : angle 4.64574 ( 2688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 213 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: A 643 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7591 (mtpp) REVERT: A 688 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6372 (tt) REVERT: A 770 MET cc_start: 0.7635 (ttm) cc_final: 0.7285 (ttm) REVERT: A 884 MET cc_start: 0.7759 (tpt) cc_final: 0.7427 (tpp) REVERT: B 443 TRP cc_start: 0.6706 (m100) cc_final: 0.5910 (m100) REVERT: B 458 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6283 (mpp) REVERT: B 472 MET cc_start: 0.7136 (mpp) cc_final: 0.6469 (mpp) REVERT: B 474 LEU cc_start: 0.8675 (mm) cc_final: 0.8327 (mt) REVERT: D 122 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5242 (tpp) REVERT: D 273 LEU cc_start: 0.7412 (tp) cc_final: 0.6622 (tt) REVERT: D 425 HIS cc_start: 0.8056 (m170) cc_final: 0.7844 (m90) REVERT: D 565 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: D 668 SER cc_start: 0.8035 (t) cc_final: 0.7702 (p) REVERT: D 781 MET cc_start: 0.6387 (ppp) cc_final: 0.6106 (ppp) REVERT: D 854 ASP cc_start: 0.6970 (p0) cc_final: 0.6526 (t0) REVERT: E 171 MET cc_start: 0.7089 (ppp) cc_final: 0.6501 (ppp) REVERT: E 416 LEU cc_start: 0.6823 (tp) cc_final: 0.6554 (mm) REVERT: E 567 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7258 (mm) REVERT: F 108 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6411 (ttm) outliers start: 100 outliers final: 67 residues processed: 293 average time/residue: 0.1461 time to fit residues: 70.1009 Evaluate side-chains 276 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 201 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 170 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 0.0060 chunk 17 optimal weight: 0.8980 chunk 219 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.183579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.146898 restraints weight = 39143.875| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.06 r_work: 0.4222 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22621 Z= 0.107 Angle : 0.580 12.834 30639 Z= 0.288 Chirality : 0.040 0.199 3528 Planarity : 0.003 0.047 3878 Dihedral : 4.811 71.743 2977 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.92 % Allowed : 20.14 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2790 helix: 1.72 (0.16), residues: 1076 sheet: -0.26 (0.22), residues: 563 loop : -1.70 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.012 0.001 TYR A 247 PHE 0.013 0.001 PHE E 557 TRP 0.015 0.001 TRP E 525 HIS 0.009 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00232 (22621) covalent geometry : angle 0.57965 (30639) hydrogen bonds : bond 0.03720 ( 925) hydrogen bonds : angle 4.49814 ( 2688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 232 time to evaluate : 1.000 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: A 99 GLN cc_start: 0.8559 (tp40) cc_final: 0.7958 (pm20) REVERT: A 326 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7356 (mt0) REVERT: A 688 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6341 (tt) REVERT: A 770 MET cc_start: 0.7607 (ttm) cc_final: 0.7278 (ttm) REVERT: A 884 MET cc_start: 0.7707 (tpt) cc_final: 0.7380 (tpp) REVERT: B 443 TRP cc_start: 0.6702 (m100) cc_final: 0.5908 (m100) REVERT: B 458 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6295 (ptp) REVERT: B 472 MET cc_start: 0.7145 (mpp) cc_final: 0.6423 (mpp) REVERT: C 101 MET cc_start: 0.2662 (OUTLIER) cc_final: 0.2177 (mpp) REVERT: D 122 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5111 (mmt) REVERT: D 225 MET cc_start: 0.6935 (mmt) cc_final: 0.6618 (mmt) REVERT: D 401 MET cc_start: 0.5046 (mtm) cc_final: 0.4779 (mtm) REVERT: D 425 HIS cc_start: 0.8107 (m170) cc_final: 0.7896 (m170) REVERT: D 553 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6486 (mm-40) REVERT: D 565 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: D 668 SER cc_start: 0.8003 (t) cc_final: 0.7677 (p) REVERT: D 781 MET cc_start: 0.6446 (ppp) cc_final: 0.6158 (ppp) REVERT: D 854 ASP cc_start: 0.6920 (p0) cc_final: 0.6497 (t0) REVERT: D 1021 GLU cc_start: 0.6499 (tt0) cc_final: 0.5855 (mt-10) REVERT: E 171 MET cc_start: 0.7033 (ppp) cc_final: 0.6484 (ppp) REVERT: E 439 ASP cc_start: 0.7126 (p0) cc_final: 0.6475 (p0) REVERT: E 567 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7236 (mm) REVERT: F 28 ARG cc_start: 0.5452 (tpt170) cc_final: 0.4761 (mtm-85) REVERT: F 108 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6254 (ttm) outliers start: 98 outliers final: 62 residues processed: 303 average time/residue: 0.1433 time to fit residues: 71.6355 Evaluate side-chains 280 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 ASN B 292 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 820 ASN D1011 ASN F 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.180648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.143587 restraints weight = 39184.693| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 3.07 r_work: 0.4169 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22621 Z= 0.152 Angle : 0.645 13.272 30639 Z= 0.320 Chirality : 0.042 0.229 3528 Planarity : 0.004 0.043 3878 Dihedral : 4.977 62.865 2977 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.44 % Allowed : 20.30 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2790 helix: 1.54 (0.15), residues: 1075 sheet: -0.45 (0.22), residues: 562 loop : -1.78 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 146 TYR 0.018 0.002 TYR D 247 PHE 0.014 0.002 PHE D 693 TRP 0.022 0.001 TRP E 525 HIS 0.015 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00348 (22621) covalent geometry : angle 0.64495 (30639) hydrogen bonds : bond 0.04458 ( 925) hydrogen bonds : angle 4.68475 ( 2688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 212 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8552 (tp40) cc_final: 0.7982 (pm20) REVERT: A 326 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: A 643 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7740 (mttm) REVERT: A 688 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6347 (tt) REVERT: A 770 MET cc_start: 0.7688 (ttm) cc_final: 0.7357 (ttm) REVERT: A 884 MET cc_start: 0.7631 (tpt) cc_final: 0.7318 (tpp) REVERT: A 973 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6863 (tt) REVERT: B 443 TRP cc_start: 0.6737 (m100) cc_final: 0.5932 (m100) REVERT: B 458 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6332 (ptp) REVERT: B 472 MET cc_start: 0.7146 (mpp) cc_final: 0.6399 (mpp) REVERT: C 101 MET cc_start: 0.2514 (OUTLIER) cc_final: 0.1978 (mpp) REVERT: D 122 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5054 (mmt) REVERT: D 401 MET cc_start: 0.5006 (mtm) cc_final: 0.4701 (mtm) REVERT: D 544 ASP cc_start: 0.8209 (t0) cc_final: 0.7959 (t0) REVERT: D 565 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: D 668 SER cc_start: 0.8083 (t) cc_final: 0.7757 (p) REVERT: D 781 MET cc_start: 0.6431 (ppp) cc_final: 0.5987 (ppp) REVERT: D 854 ASP cc_start: 0.7020 (p0) cc_final: 0.6569 (t0) REVERT: D 863 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8014 (tt) REVERT: E 171 MET cc_start: 0.7213 (ppp) cc_final: 0.7006 (ppp) REVERT: E 491 GLN cc_start: 0.6242 (tt0) cc_final: 0.5739 (tt0) REVERT: E 567 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7293 (mm) REVERT: F 108 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6396 (ttm) outliers start: 111 outliers final: 77 residues processed: 299 average time/residue: 0.1265 time to fit residues: 62.7360 Evaluate side-chains 292 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 204 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 141 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 222 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 88 optimal weight: 0.0000 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.183633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.147173 restraints weight = 38953.366| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.05 r_work: 0.4229 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22621 Z= 0.105 Angle : 0.602 13.819 30639 Z= 0.295 Chirality : 0.040 0.222 3528 Planarity : 0.003 0.049 3878 Dihedral : 4.734 63.164 2977 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.48 % Allowed : 20.94 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 2790 helix: 1.69 (0.16), residues: 1076 sheet: -0.33 (0.22), residues: 566 loop : -1.69 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.016 0.001 TYR D 247 PHE 0.013 0.001 PHE B 278 TRP 0.016 0.001 TRP E 525 HIS 0.013 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00226 (22621) covalent geometry : angle 0.60219 (30639) hydrogen bonds : bond 0.03555 ( 925) hydrogen bonds : angle 4.45527 ( 2688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 222 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8522 (tp40) cc_final: 0.7914 (pm20) REVERT: A 104 HIS cc_start: 0.4269 (OUTLIER) cc_final: 0.3957 (p-80) REVERT: A 326 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: A 578 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4786 (mp) REVERT: A 688 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6248 (tt) REVERT: A 770 MET cc_start: 0.7618 (ttm) cc_final: 0.7282 (ttm) REVERT: A 884 MET cc_start: 0.7648 (tpt) cc_final: 0.7326 (tpp) REVERT: A 964 LYS cc_start: 0.7532 (tmmt) cc_final: 0.7253 (pptt) REVERT: B 277 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7296 (mmp-170) REVERT: B 443 TRP cc_start: 0.6685 (m100) cc_final: 0.5877 (m100) REVERT: B 458 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6250 (ptp) REVERT: B 472 MET cc_start: 0.7296 (mpp) cc_final: 0.6541 (mpp) REVERT: C 101 MET cc_start: 0.2537 (OUTLIER) cc_final: 0.2177 (mpp) REVERT: D 122 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5306 (mmt) REVERT: D 255 ARG cc_start: 0.5832 (mmp80) cc_final: 0.5596 (mtm180) REVERT: D 401 MET cc_start: 0.5026 (mtm) cc_final: 0.4732 (mtm) REVERT: D 553 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6494 (mm-40) REVERT: D 565 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: D 668 SER cc_start: 0.8013 (t) cc_final: 0.7749 (p) REVERT: D 781 MET cc_start: 0.6417 (ppp) cc_final: 0.5966 (ppp) REVERT: D 854 ASP cc_start: 0.6851 (p0) cc_final: 0.6451 (t0) REVERT: E 171 MET cc_start: 0.7039 (ppp) cc_final: 0.6542 (ppp) REVERT: E 567 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7190 (mm) REVERT: F 28 ARG cc_start: 0.5452 (tpt170) cc_final: 0.4796 (mtm-85) REVERT: F 108 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6357 (ttm) outliers start: 87 outliers final: 59 residues processed: 291 average time/residue: 0.1224 time to fit residues: 58.8480 Evaluate side-chains 286 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 4 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 119 optimal weight: 0.0060 chunk 112 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.182982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.146430 restraints weight = 39016.718| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.07 r_work: 0.4207 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22621 Z= 0.112 Angle : 0.620 13.967 30639 Z= 0.301 Chirality : 0.040 0.188 3528 Planarity : 0.003 0.049 3878 Dihedral : 4.539 54.144 2974 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.52 % Allowed : 21.18 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2790 helix: 1.66 (0.16), residues: 1078 sheet: -0.34 (0.22), residues: 567 loop : -1.69 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 100 TYR 0.026 0.001 TYR D 251 PHE 0.012 0.001 PHE D 173 TRP 0.016 0.001 TRP E 525 HIS 0.012 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00248 (22621) covalent geometry : angle 0.61981 (30639) hydrogen bonds : bond 0.03680 ( 925) hydrogen bonds : angle 4.46305 ( 2688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 221 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8521 (tp40) cc_final: 0.7907 (pm20) REVERT: A 326 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: A 578 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4695 (mp) REVERT: A 688 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6247 (tt) REVERT: A 744 MET cc_start: 0.6216 (mmp) cc_final: 0.5778 (mtt) REVERT: A 770 MET cc_start: 0.7661 (ttm) cc_final: 0.7322 (ttm) REVERT: A 884 MET cc_start: 0.7687 (tpt) cc_final: 0.7366 (tpp) REVERT: B 277 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7359 (mmp-170) REVERT: B 443 TRP cc_start: 0.6706 (m100) cc_final: 0.5897 (m100) REVERT: B 458 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6339 (ptp) REVERT: B 472 MET cc_start: 0.7256 (mpp) cc_final: 0.6545 (mpp) REVERT: C 101 MET cc_start: 0.2452 (OUTLIER) cc_final: 0.2190 (mpp) REVERT: D 122 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5249 (tpp) REVERT: D 255 ARG cc_start: 0.5843 (mmp80) cc_final: 0.5527 (mmt180) REVERT: D 401 MET cc_start: 0.4967 (mtm) cc_final: 0.4406 (mtm) REVERT: D 425 HIS cc_start: 0.8142 (m170) cc_final: 0.7936 (m170) REVERT: D 487 ARG cc_start: 0.7248 (ptt-90) cc_final: 0.6921 (ptt-90) REVERT: D 565 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: D 668 SER cc_start: 0.8097 (t) cc_final: 0.7781 (p) REVERT: D 781 MET cc_start: 0.6445 (ppp) cc_final: 0.6130 (ppp) REVERT: D 854 ASP cc_start: 0.6886 (p0) cc_final: 0.6467 (t0) REVERT: E 171 MET cc_start: 0.7093 (ppp) cc_final: 0.6581 (ppp) REVERT: E 567 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7207 (mm) REVERT: F 108 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6389 (ttm) outliers start: 88 outliers final: 66 residues processed: 287 average time/residue: 0.1346 time to fit residues: 63.2481 Evaluate side-chains 292 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 217 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 6 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 235 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 227 optimal weight: 0.2980 chunk 246 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 187 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.184377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.149762 restraints weight = 39228.563| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 3.29 r_work: 0.4224 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22621 Z= 0.103 Angle : 0.617 14.438 30639 Z= 0.298 Chirality : 0.040 0.287 3528 Planarity : 0.003 0.049 3878 Dihedral : 4.435 52.765 2974 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.00 % Allowed : 21.58 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2790 helix: 1.69 (0.16), residues: 1080 sheet: -0.29 (0.22), residues: 560 loop : -1.64 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1025 TYR 0.033 0.001 TYR D 251 PHE 0.011 0.001 PHE D 366 TRP 0.019 0.001 TRP F 111 HIS 0.012 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00223 (22621) covalent geometry : angle 0.61722 (30639) hydrogen bonds : bond 0.03373 ( 925) hydrogen bonds : angle 4.36820 ( 2688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 226 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8524 (tp40) cc_final: 0.7949 (pm20) REVERT: A 326 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: A 578 LEU cc_start: 0.4938 (OUTLIER) cc_final: 0.4616 (mp) REVERT: A 688 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6251 (tt) REVERT: A 744 MET cc_start: 0.6330 (mmp) cc_final: 0.5842 (mtt) REVERT: A 770 MET cc_start: 0.7635 (ttm) cc_final: 0.7326 (ttm) REVERT: A 884 MET cc_start: 0.7661 (tpt) cc_final: 0.7336 (tpp) REVERT: A 964 LYS cc_start: 0.7493 (tmmt) cc_final: 0.7228 (pptt) REVERT: B 277 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7377 (mmp-170) REVERT: B 443 TRP cc_start: 0.6681 (m100) cc_final: 0.5887 (m100) REVERT: B 458 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6359 (ptp) REVERT: B 472 MET cc_start: 0.7250 (mpp) cc_final: 0.6515 (mpp) REVERT: D 122 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5453 (tpp) REVERT: D 255 ARG cc_start: 0.5918 (mmp80) cc_final: 0.5673 (mtm180) REVERT: D 401 MET cc_start: 0.4984 (mtm) cc_final: 0.4407 (mtm) REVERT: D 487 ARG cc_start: 0.7288 (ptt-90) cc_final: 0.7063 (ptt-90) REVERT: D 565 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: D 668 SER cc_start: 0.8113 (t) cc_final: 0.7782 (p) REVERT: D 781 MET cc_start: 0.6390 (ppp) cc_final: 0.6068 (ppp) REVERT: D 854 ASP cc_start: 0.6857 (p0) cc_final: 0.6448 (t0) REVERT: E 171 MET cc_start: 0.7031 (ppp) cc_final: 0.6824 (ppp) REVERT: E 482 TRP cc_start: 0.6805 (m100) cc_final: 0.6520 (m100) REVERT: E 567 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7184 (mm) REVERT: F 28 ARG cc_start: 0.5464 (tpt170) cc_final: 0.4764 (mtm-85) REVERT: F 108 MET cc_start: 0.7404 (mmp) cc_final: 0.6531 (ttm) outliers start: 75 outliers final: 56 residues processed: 283 average time/residue: 0.1273 time to fit residues: 59.0791 Evaluate side-chains 280 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 240 optimal weight: 0.0770 chunk 168 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 292 HIS B 434 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.184444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.149983 restraints weight = 38837.601| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.28 r_work: 0.4226 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22621 Z= 0.104 Angle : 0.618 14.281 30639 Z= 0.299 Chirality : 0.041 0.260 3528 Planarity : 0.003 0.050 3878 Dihedral : 4.382 52.250 2973 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.96 % Allowed : 21.82 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2790 helix: 1.68 (0.16), residues: 1079 sheet: -0.38 (0.22), residues: 577 loop : -1.59 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.032 0.001 TYR D 251 PHE 0.030 0.001 PHE A 109 TRP 0.018 0.001 TRP E 525 HIS 0.011 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00226 (22621) covalent geometry : angle 0.61833 (30639) hydrogen bonds : bond 0.03348 ( 925) hydrogen bonds : angle 4.36826 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6243.78 seconds wall clock time: 107 minutes 47.01 seconds (6467.01 seconds total)