Starting phenix.real_space_refine on Thu Jun 19 10:57:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h93_34552/06_2025/8h93_34552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h93_34552/06_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_34552/06_2025/8h93_34552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h93_34552/06_2025/8h93_34552.map" model { file = "/net/cci-nas-00/data/ceres_data/8h93_34552/06_2025/8h93_34552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h93_34552/06_2025/8h93_34552.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS: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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS: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: 13.74, per 1000 atoms: 0.62 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: 5.82 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.93 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: 9.72 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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: 0.010 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 53.990 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.940 ------------------------------------------------------------------------------- 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 : 12.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (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 TRP 0.035 0.001 TRP A 629 HIS 0.008 0.001 HIS A 104 PHE 0.025 0.001 PHE D 177 TYR 0.014 0.001 TYR D1023 ARG 0.006 0.000 ARG F 100 Details of bonding type rmsd hydrogen bonds : bond 0.25796 ( 925) hydrogen bonds : angle 7.32448 ( 2688) covalent geometry : bond 0.00342 (22621) covalent geometry : angle 0.67921 (30639) *********************** 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 : 2.438 Fit side-chains 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 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: 0.6900 (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: 8 residues processed: 334 average time/residue: 0.3575 time to fit residues: 185.9202 Evaluate side-chains 234 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 optimal weight: 2.9990 chunk 209 optimal weight: 0.3980 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 161 optimal weight: 0.0470 chunk 250 optimal weight: 0.9980 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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** B 532 ASN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.186654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.149710 restraints weight = 38590.428| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.15 r_work: 0.4260 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22621 Z= 0.127 Angle : 0.619 11.393 30639 Z= 0.314 Chirality : 0.041 0.234 3528 Planarity : 0.004 0.088 3878 Dihedral : 5.185 89.941 2987 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.28 % Allowed : 14.85 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2790 helix: 1.83 (0.15), residues: 1078 sheet: 0.08 (0.22), residues: 568 loop : -1.49 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 525 HIS 0.018 0.001 HIS A 425 PHE 0.016 0.001 PHE E 557 TYR 0.016 0.002 TYR A 247 ARG 0.010 0.001 ARG E 412 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 925) hydrogen bonds : angle 5.18536 ( 2688) covalent geometry : bond 0.00263 (22621) covalent geometry : angle 0.61897 (30639) *********************** 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 307 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8461 (tp40) cc_final: 0.7702 (pm20) REVERT: A 279 MET cc_start: 0.5593 (pmm) cc_final: 0.5276 (mtm) REVERT: A 629 TRP cc_start: 0.4724 (t-100) cc_final: 0.4446 (t-100) REVERT: A 699 LYS cc_start: 0.7788 (mppt) cc_final: 0.7438 (mppt) REVERT: A 770 MET cc_start: 0.7603 (ttm) cc_final: 0.7270 (ttm) REVERT: A 973 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6938 (tt) REVERT: B 171 MET cc_start: 0.6931 (tpp) cc_final: 0.5487 (tmm) REVERT: B 277 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7621 (mmp-170) REVERT: B 295 LEU cc_start: 0.4344 (OUTLIER) cc_final: 0.3935 (tp) REVERT: B 443 TRP cc_start: 0.6331 (m100) cc_final: 0.5665 (m100) REVERT: B 458 MET cc_start: 0.6331 (ppp) cc_final: 0.5656 (mmt) REVERT: D 122 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5103 (mmt) REVERT: D 137 GLN cc_start: 0.6729 (tm-30) cc_final: 0.6344 (tm-30) REVERT: D 273 LEU cc_start: 0.7592 (tp) cc_final: 0.6997 (tt) REVERT: D 401 MET cc_start: 0.4874 (mtt) cc_final: 0.4587 (mtm) REVERT: D 487 ARG cc_start: 0.7479 (ptp-170) cc_final: 0.7254 (ptp-170) REVERT: D 553 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6567 (mm-40) REVERT: D 565 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: D 622 LYS cc_start: 0.6038 (tppt) cc_final: 0.5608 (tttp) REVERT: D 657 MET cc_start: 0.8095 (tpt) cc_final: 0.7849 (tpt) REVERT: D 668 SER cc_start: 0.7899 (t) cc_final: 0.7669 (t) REVERT: D 744 MET cc_start: 0.7835 (mpp) cc_final: 0.7205 (mtt) REVERT: D 781 MET cc_start: 0.6409 (ppp) cc_final: 0.6030 (ppp) REVERT: D 854 ASP cc_start: 0.7043 (p0) cc_final: 0.6611 (t0) REVERT: D 919 MET cc_start: 0.7323 (tmm) cc_final: 0.6958 (tmm) REVERT: D 1021 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5571 (mt-10) REVERT: E 439 ASP cc_start: 0.7215 (p0) cc_final: 0.6577 (p0) REVERT: E 493 CYS cc_start: 0.7376 (m) cc_final: 0.7001 (t) REVERT: F 49 MET cc_start: 0.6472 (mmm) cc_final: 0.6217 (mpp) REVERT: F 108 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6457 (ttm) outliers start: 57 outliers final: 25 residues processed: 291 average time/residue: 0.3315 time to fit residues: 156.4429 Evaluate side-chains 248 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS 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 604 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 295 LEU Chi-restraints excluded: chain B residue 298 VAL 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 470 PHE 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 D residue 1017 LEU 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 36 optimal weight: 5.9990 chunk 188 optimal weight: 0.0870 chunk 88 optimal weight: 0.3980 chunk 166 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 0.0070 chunk 102 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.186724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.151658 restraints weight = 38751.996| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 3.50 r_work: 0.4251 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22621 Z= 0.107 Angle : 0.568 11.341 30639 Z= 0.285 Chirality : 0.040 0.198 3528 Planarity : 0.003 0.046 3878 Dihedral : 4.501 56.551 2975 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.52 % Allowed : 16.93 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2790 helix: 1.90 (0.15), residues: 1074 sheet: 0.03 (0.22), residues: 577 loop : -1.49 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 525 HIS 0.009 0.001 HIS A 425 PHE 0.019 0.001 PHE B 278 TYR 0.019 0.001 TYR A 247 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 925) hydrogen bonds : angle 4.71741 ( 2688) covalent geometry : bond 0.00218 (22621) covalent geometry : angle 0.56829 (30639) *********************** 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 305 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8540 (tp40) cc_final: 0.7915 (pm20) REVERT: A 708 MET cc_start: 0.7606 (tpt) cc_final: 0.7362 (tpt) REVERT: A 770 MET cc_start: 0.7578 (ttm) cc_final: 0.7241 (ttm) REVERT: B 277 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7630 (mmp-170) REVERT: B 443 TRP cc_start: 0.6362 (m100) cc_final: 0.5665 (m100) REVERT: B 458 MET cc_start: 0.6697 (ppp) cc_final: 0.6183 (mtm) REVERT: D 122 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4990 (mmt) REVERT: D 137 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6860 (tm-30) REVERT: D 273 LEU cc_start: 0.7557 (tp) cc_final: 0.6949 (tt) REVERT: D 401 MET cc_start: 0.4833 (mtt) cc_final: 0.4438 (mtm) REVERT: D 487 ARG cc_start: 0.7511 (ptp-170) cc_final: 0.7151 (ptt-90) REVERT: D 565 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: D 622 LYS cc_start: 0.5885 (tppt) cc_final: 0.5568 (tttp) REVERT: D 668 SER cc_start: 0.7924 (t) cc_final: 0.7690 (t) REVERT: D 744 MET cc_start: 0.7626 (mpp) cc_final: 0.7090 (mtt) REVERT: D 770 MET cc_start: 0.8452 (tpp) cc_final: 0.8113 (tpt) REVERT: D 781 MET cc_start: 0.6192 (ppp) cc_final: 0.5905 (ppp) REVERT: D 854 ASP cc_start: 0.6882 (p0) cc_final: 0.6525 (t0) REVERT: D 919 MET cc_start: 0.7456 (tmm) cc_final: 0.6760 (tmm) REVERT: D 1021 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5679 (mt-10) REVERT: E 439 ASP cc_start: 0.7165 (p0) cc_final: 0.6525 (p0) REVERT: E 493 CYS cc_start: 0.7414 (m) cc_final: 0.7054 (t) REVERT: E 505 THR cc_start: 0.7852 (p) cc_final: 0.7449 (m) REVERT: F 28 ARG cc_start: 0.5317 (tpt170) cc_final: 0.4774 (mtm-85) REVERT: F 49 MET cc_start: 0.7023 (mmm) cc_final: 0.6740 (mmt) REVERT: F 108 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6432 (ttm) outliers start: 63 outliers final: 33 residues processed: 286 average time/residue: 0.3760 time to fit residues: 175.2325 Evaluate side-chains 251 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP 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 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 407 THR 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 173 PHE 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 317 LEU Chi-restraints excluded: chain D residue 470 PHE 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 859 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 298 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 86 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 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 303 ASN D1011 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.185557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.148882 restraints weight = 38959.014| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 3.05 r_work: 0.4238 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22621 Z= 0.110 Angle : 0.572 12.001 30639 Z= 0.284 Chirality : 0.040 0.186 3528 Planarity : 0.003 0.042 3878 Dihedral : 4.489 57.555 2975 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.96 % Allowed : 18.09 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2790 helix: 1.90 (0.16), residues: 1076 sheet: -0.21 (0.21), residues: 607 loop : -1.44 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 525 HIS 0.012 0.001 HIS A 425 PHE 0.022 0.001 PHE E 557 TYR 0.015 0.001 TYR A 247 ARG 0.004 0.000 ARG E 571 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 925) hydrogen bonds : angle 4.57520 ( 2688) covalent geometry : bond 0.00236 (22621) covalent geometry : angle 0.57249 (30639) *********************** 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 297 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 3.602 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: 0.8540 (tp40) cc_final: 0.7929 (pm20) REVERT: A 101 TYR cc_start: 0.6589 (t80) cc_final: 0.6265 (t80) REVERT: A 708 MET cc_start: 0.7668 (tpt) cc_final: 0.7400 (tpt) REVERT: A 770 MET cc_start: 0.7589 (ttm) cc_final: 0.7256 (ttm) REVERT: A 884 MET cc_start: 0.7711 (tpt) cc_final: 0.7502 (tpp) REVERT: B 443 TRP cc_start: 0.6475 (m100) cc_final: 0.5793 (m100) REVERT: D 122 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.4988 (tpp) REVERT: D 137 GLN cc_start: 0.6861 (tm-30) cc_final: 0.6607 (tm-30) REVERT: D 171 MET cc_start: 0.4312 (mtt) cc_final: 0.3936 (mtt) REVERT: D 273 LEU cc_start: 0.7522 (tp) cc_final: 0.6879 (tt) REVERT: D 425 HIS cc_start: 0.7999 (m170) cc_final: 0.7781 (m90) REVERT: D 487 ARG cc_start: 0.7506 (ptp-170) cc_final: 0.7228 (ptt-90) REVERT: D 553 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6089 (mm-40) REVERT: D 565 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: D 668 SER cc_start: 0.7896 (t) cc_final: 0.7684 (t) REVERT: D 744 MET cc_start: 0.7410 (mpp) cc_final: 0.7208 (mpp) REVERT: D 770 MET cc_start: 0.8428 (tpp) cc_final: 0.8067 (tpt) REVERT: D 781 MET cc_start: 0.6345 (ppp) cc_final: 0.6096 (ppp) REVERT: D 854 ASP cc_start: 0.6863 (p0) cc_final: 0.6530 (t0) REVERT: D 1021 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5672 (mt-10) REVERT: E 439 ASP cc_start: 0.7200 (p0) cc_final: 0.6571 (p0) REVERT: E 493 CYS cc_start: 0.7441 (m) cc_final: 0.7053 (t) REVERT: E 505 THR cc_start: 0.7781 (p) cc_final: 0.7416 (m) REVERT: E 567 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7214 (mm) REVERT: F 28 ARG cc_start: 0.5372 (tpt170) cc_final: 0.4804 (mtm-85) REVERT: F 108 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6345 (ttm) outliers start: 74 outliers final: 44 residues processed: 276 average time/residue: 0.3636 time to fit residues: 167.0647 Evaluate side-chains 251 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 2.530 ------------------------------------------------------------------------------- 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 350 CYS Chi-restraints excluded: chain A residue 366 PHE 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 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 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 507 ASP 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 D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 173 PHE 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 317 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 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 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 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 130 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 188 optimal weight: 0.0570 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- 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 574 GLN B 292 HIS B 323 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D1011 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.179854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.142610 restraints weight = 39381.626| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.05 r_work: 0.4164 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.005 0.070 22621 Z= 0.202 Angle : 0.695 12.134 30639 Z= 0.349 Chirality : 0.044 0.226 3528 Planarity : 0.004 0.042 3878 Dihedral : 4.989 58.327 2974 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.80 % Allowed : 18.49 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 2790 helix: 1.50 (0.15), residues: 1082 sheet: -0.43 (0.21), residues: 579 loop : -1.72 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 525 HIS 0.015 0.002 HIS A 425 PHE 0.032 0.002 PHE D 366 TYR 0.019 0.002 TYR E 577 ARG 0.006 0.001 ARG C 100 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 925) hydrogen bonds : angle 4.89925 ( 2688) covalent geometry : bond 0.00466 (22621) covalent geometry : angle 0.69492 (30639) *********************** 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 305 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 210 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6459 (tt) REVERT: A 708 MET cc_start: 0.7541 (tpt) cc_final: 0.7255 (tpt) REVERT: A 770 MET cc_start: 0.7713 (ttm) cc_final: 0.7362 (ttm) REVERT: A 884 MET cc_start: 0.7681 (tpt) cc_final: 0.7361 (tpp) REVERT: A 964 LYS cc_start: 0.8017 (tmmt) cc_final: 0.7507 (pttm) REVERT: A 973 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6914 (tt) REVERT: B 295 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.4029 (tp) REVERT: B 443 TRP cc_start: 0.6774 (m100) cc_final: 0.6018 (m100) REVERT: B 458 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6315 (mpp) REVERT: B 472 MET cc_start: 0.7064 (mpp) cc_final: 0.6413 (mpp) REVERT: C 101 MET cc_start: 0.2121 (OUTLIER) cc_final: 0.1526 (mpp) REVERT: D 122 MET cc_start: 0.5881 (OUTLIER) cc_final: 0.5208 (tpp) REVERT: D 137 GLN cc_start: 0.7290 (tm-30) cc_final: 0.6961 (tm-30) REVERT: D 425 HIS cc_start: 0.8191 (m170) cc_final: 0.7926 (m170) REVERT: D 487 ARG cc_start: 0.7564 (ptp-170) cc_final: 0.7306 (ptp-170) REVERT: D 544 ASP cc_start: 0.8239 (t0) cc_final: 0.7987 (t0) REVERT: D 553 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6507 (mm-40) REVERT: D 565 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: D 668 SER cc_start: 0.8033 (t) cc_final: 0.7664 (p) REVERT: D 854 ASP cc_start: 0.7061 (p0) cc_final: 0.6609 (t0) REVERT: E 416 LEU cc_start: 0.6819 (tp) cc_final: 0.6512 (mm) REVERT: E 567 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7375 (mm) REVERT: F 49 MET cc_start: 0.6691 (mpp) cc_final: 0.6478 (mmt) REVERT: F 108 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6504 (ttm) outliers start: 95 outliers final: 61 residues processed: 282 average time/residue: 0.2993 time to fit residues: 139.5759 Evaluate side-chains 267 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 196 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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 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 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 B residue 146 ASP 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 323 ASN 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 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 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 317 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 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 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 1012 LEU Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 382 CYS 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 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 87 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D1011 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.182854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.145978 restraints weight = 38891.922| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.05 r_work: 0.4203 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22621 Z= 0.114 Angle : 0.597 13.257 30639 Z= 0.297 Chirality : 0.040 0.195 3528 Planarity : 0.003 0.046 3878 Dihedral : 4.684 56.537 2974 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.20 % Allowed : 19.94 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2790 helix: 1.68 (0.16), residues: 1073 sheet: -0.44 (0.21), residues: 597 loop : -1.66 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 525 HIS 0.012 0.001 HIS A 425 PHE 0.012 0.001 PHE D 173 TYR 0.012 0.001 TYR A 247 ARG 0.004 0.000 ARG C 100 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 925) hydrogen bonds : angle 4.60490 ( 2688) covalent geometry : bond 0.00247 (22621) covalent geometry : angle 0.59680 (30639) *********************** 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 295 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 215 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8543 (tp40) cc_final: 0.7952 (pm20) REVERT: A 234 MET cc_start: 0.4463 (ppp) cc_final: 0.4076 (ppp) REVERT: A 688 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6308 (tt) REVERT: A 770 MET cc_start: 0.7657 (ttm) cc_final: 0.7323 (ttm) REVERT: A 884 MET cc_start: 0.7689 (tpt) cc_final: 0.7366 (tpp) REVERT: A 964 LYS cc_start: 0.7998 (tmmt) cc_final: 0.7531 (pttm) REVERT: B 443 TRP cc_start: 0.6739 (m100) cc_final: 0.5990 (m100) REVERT: B 458 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6308 (ptp) REVERT: B 472 MET cc_start: 0.7006 (mpp) cc_final: 0.6283 (mpp) REVERT: D 122 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5139 (tpp) REVERT: D 137 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6675 (tm-30) REVERT: D 171 MET cc_start: 0.5031 (mtt) cc_final: 0.4622 (mtp) REVERT: D 273 LEU cc_start: 0.7466 (tp) cc_final: 0.6710 (tt) REVERT: D 425 HIS cc_start: 0.8124 (m170) cc_final: 0.7896 (m170) REVERT: D 487 ARG cc_start: 0.7512 (ptp-170) cc_final: 0.7217 (ptp-170) REVERT: D 544 ASP cc_start: 0.8131 (t0) cc_final: 0.7869 (t0) REVERT: D 553 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6433 (mm-40) REVERT: D 565 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: D 668 SER cc_start: 0.8012 (t) cc_final: 0.7669 (p) REVERT: D 854 ASP cc_start: 0.6934 (p0) cc_final: 0.6511 (t0) REVERT: E 567 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7218 (mm) REVERT: F 28 ARG cc_start: 0.5530 (tpt170) cc_final: 0.4862 (mtm-85) REVERT: F 49 MET cc_start: 0.6666 (mpp) cc_final: 0.6448 (mmt) REVERT: F 108 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6365 (ttm) outliers start: 80 outliers final: 53 residues processed: 277 average time/residue: 0.2966 time to fit residues: 133.8050 Evaluate side-chains 263 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 2.345 ------------------------------------------------------------------------------- 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 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 B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP 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 53 VAL Chi-restraints excluded: chain C residue 81 VAL 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 224 ASP 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 317 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 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 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 328 ASP Chi-restraints excluded: chain E residue 461 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 261 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 206 optimal weight: 0.0170 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.182199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.145442 restraints weight = 38975.575| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.05 r_work: 0.4206 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22621 Z= 0.124 Angle : 0.611 13.195 30639 Z= 0.302 Chirality : 0.041 0.226 3528 Planarity : 0.004 0.045 3878 Dihedral : 4.657 56.235 2974 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.92 % Allowed : 19.54 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2790 helix: 1.63 (0.16), residues: 1077 sheet: -0.43 (0.21), residues: 560 loop : -1.70 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 525 HIS 0.010 0.001 HIS A 425 PHE 0.012 0.001 PHE D 173 TYR 0.014 0.001 TYR D 247 ARG 0.003 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 925) hydrogen bonds : angle 4.56345 ( 2688) covalent geometry : bond 0.00277 (22621) covalent geometry : angle 0.61075 (30639) *********************** 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 314 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 216 time to evaluate : 2.510 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: 0.8537 (tp40) cc_final: 0.7969 (pm20) REVERT: A 234 MET cc_start: 0.4594 (ppp) cc_final: 0.4383 (ppp) REVERT: A 688 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6347 (tt) REVERT: A 770 MET cc_start: 0.7665 (ttm) cc_final: 0.7332 (ttm) REVERT: A 884 MET cc_start: 0.7671 (tpt) cc_final: 0.7356 (tpp) REVERT: A 964 LYS cc_start: 0.8095 (tmmt) cc_final: 0.7656 (pttm) REVERT: B 443 TRP cc_start: 0.6724 (m100) cc_final: 0.5953 (m100) REVERT: B 458 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6301 (ptp) REVERT: B 472 MET cc_start: 0.7052 (mpp) cc_final: 0.6335 (mpp) REVERT: C 101 MET cc_start: 0.1274 (OUTLIER) cc_final: 0.0675 (mpp) REVERT: D 122 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5181 (tpp) REVERT: D 273 LEU cc_start: 0.7513 (tp) cc_final: 0.6715 (tt) REVERT: D 425 HIS cc_start: 0.8167 (m170) cc_final: 0.7921 (m170) REVERT: D 487 ARG cc_start: 0.7583 (ptp-170) cc_final: 0.7268 (ptp-170) REVERT: D 544 ASP cc_start: 0.8153 (t0) cc_final: 0.7897 (t0) REVERT: D 553 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6465 (mm-40) REVERT: D 565 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: D 668 SER cc_start: 0.8019 (t) cc_final: 0.7692 (p) REVERT: D 854 ASP cc_start: 0.6945 (p0) cc_final: 0.6528 (t0) REVERT: E 567 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7211 (mm) REVERT: F 49 MET cc_start: 0.6698 (mpp) cc_final: 0.6472 (mmt) REVERT: F 108 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6308 (ttm) outliers start: 98 outliers final: 67 residues processed: 291 average time/residue: 0.3081 time to fit residues: 146.6799 Evaluate side-chains 282 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 207 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 324 PHE 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 558 VAL 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 955 LEU Chi-restraints excluded: chain A residue 973 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 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 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 317 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 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 601 LEU 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 E residue 328 ASP Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain E residue 416 LEU 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 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 156 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 230 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 425 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN 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 = 0.4758 r_free = 0.4758 target = 0.183730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.147256 restraints weight = 39098.587| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 3.05 r_work: 0.4227 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22621 Z= 0.106 Angle : 0.597 13.481 30639 Z= 0.293 Chirality : 0.040 0.241 3528 Planarity : 0.003 0.048 3878 Dihedral : 4.503 54.909 2974 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.32 % Allowed : 20.38 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2790 helix: 1.76 (0.16), residues: 1072 sheet: -0.37 (0.21), residues: 572 loop : -1.68 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 111 HIS 0.020 0.001 HIS A 425 PHE 0.011 0.001 PHE D 173 TYR 0.016 0.001 TYR D 247 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 925) hydrogen bonds : angle 4.43435 ( 2688) covalent geometry : bond 0.00230 (22621) covalent geometry : angle 0.59732 (30639) *********************** 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 303 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 220 time to evaluate : 2.717 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: 0.8542 (tp40) cc_final: 0.8007 (pm20) REVERT: A 234 MET cc_start: 0.4410 (ppp) cc_final: 0.4121 (ppp) REVERT: A 688 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6244 (tt) REVERT: A 770 MET cc_start: 0.7658 (ttm) cc_final: 0.7321 (ttm) REVERT: A 884 MET cc_start: 0.7675 (tpt) cc_final: 0.7344 (tpp) REVERT: A 964 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7692 (pttm) REVERT: B 443 TRP cc_start: 0.6709 (m100) cc_final: 0.5935 (m100) REVERT: B 458 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6332 (ptp) REVERT: B 472 MET cc_start: 0.7135 (mpp) cc_final: 0.6434 (mpp) REVERT: D 122 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5349 (tpp) REVERT: D 255 ARG cc_start: 0.5838 (mmp80) cc_final: 0.5588 (mtm180) REVERT: D 425 HIS cc_start: 0.8158 (m170) cc_final: 0.7915 (m170) REVERT: D 448 GLN cc_start: 0.8491 (tp-100) cc_final: 0.7379 (tm-30) REVERT: D 487 ARG cc_start: 0.7514 (ptp-170) cc_final: 0.7245 (ptp-170) REVERT: D 553 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6473 (mm-40) REVERT: D 565 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: D 668 SER cc_start: 0.8010 (t) cc_final: 0.7743 (p) REVERT: D 854 ASP cc_start: 0.6861 (p0) cc_final: 0.6451 (t0) REVERT: E 493 CYS cc_start: 0.7549 (m) cc_final: 0.7022 (t) REVERT: E 567 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7230 (mm) REVERT: F 28 ARG cc_start: 0.5432 (tpt170) cc_final: 0.4748 (mtm-85) REVERT: F 49 MET cc_start: 0.6696 (mpp) cc_final: 0.6477 (mmt) REVERT: F 108 MET cc_start: 0.7253 (mmp) cc_final: 0.6304 (ttm) outliers start: 83 outliers final: 61 residues processed: 281 average time/residue: 0.3089 time to fit residues: 139.6951 Evaluate side-chains 277 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 324 PHE 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 558 VAL 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 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 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 53 VAL Chi-restraints excluded: chain C residue 81 VAL 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 139 HIS 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 317 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 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 E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU 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 112 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 175 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 819 ASN B 292 HIS B 323 ASN B 383 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN F 112 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.179856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.144077 restraints weight = 39669.464| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.85 r_work: 0.4200 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22621 Z= 0.182 Angle : 0.683 13.218 30639 Z= 0.341 Chirality : 0.043 0.247 3528 Planarity : 0.004 0.044 3878 Dihedral : 4.892 56.727 2974 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.64 % Allowed : 20.14 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2790 helix: 1.42 (0.15), residues: 1075 sheet: -0.64 (0.22), residues: 567 loop : -1.80 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 525 HIS 0.026 0.002 HIS F 112 PHE 0.016 0.002 PHE D 173 TYR 0.020 0.002 TYR E 577 ARG 0.004 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 925) hydrogen bonds : angle 4.76847 ( 2688) covalent geometry : bond 0.00418 (22621) covalent geometry : angle 0.68344 (30639) *********************** 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 300 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 209 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8516 (tp40) cc_final: 0.7957 (pm20) REVERT: A 688 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6561 (tt) REVERT: A 770 MET cc_start: 0.7544 (ttm) cc_final: 0.7214 (ttm) REVERT: A 884 MET cc_start: 0.7454 (tpt) cc_final: 0.7177 (tpp) REVERT: A 964 LYS cc_start: 0.8139 (tmmt) cc_final: 0.7841 (pttm) REVERT: A 973 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6850 (tt) REVERT: B 443 TRP cc_start: 0.6913 (m100) cc_final: 0.6096 (m100) REVERT: B 458 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6243 (ptp) REVERT: B 472 MET cc_start: 0.7319 (mpp) cc_final: 0.6580 (mpp) REVERT: C 101 MET cc_start: 0.1793 (OUTLIER) cc_final: 0.0578 (mpp) REVERT: D 122 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5341 (tpp) REVERT: D 247 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.6195 (p90) REVERT: D 487 ARG cc_start: 0.7555 (ptp-170) cc_final: 0.7321 (ptp-170) REVERT: D 565 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: D 668 SER cc_start: 0.7914 (t) cc_final: 0.7661 (p) REVERT: D 854 ASP cc_start: 0.6832 (p0) cc_final: 0.6539 (t0) REVERT: E 443 TRP cc_start: 0.7089 (m100) cc_final: 0.6485 (m100) REVERT: E 567 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7351 (mm) REVERT: F 49 MET cc_start: 0.6811 (mpp) cc_final: 0.6558 (mmt) REVERT: F 108 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6399 (ttm) outliers start: 91 outliers final: 70 residues processed: 279 average time/residue: 0.3031 time to fit residues: 136.7862 Evaluate side-chains 283 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 204 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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 324 PHE 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 558 VAL 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 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 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 323 ASN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 383 GLN 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 139 HIS 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 247 TYR 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 317 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 601 LEU Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 730 LEU 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 E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain E residue 416 LEU 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 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 263 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.181881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.145184 restraints weight = 39075.704| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.06 r_work: 0.4200 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22621 Z= 0.120 Angle : 0.634 13.714 30639 Z= 0.311 Chirality : 0.041 0.248 3528 Planarity : 0.004 0.047 3878 Dihedral : 4.722 56.026 2974 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.16 % Allowed : 20.54 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2790 helix: 1.51 (0.16), residues: 1076 sheet: -0.51 (0.22), residues: 555 loop : -1.79 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 525 HIS 0.007 0.001 HIS D 231 PHE 0.012 0.001 PHE D 173 TYR 0.017 0.001 TYR D 247 ARG 0.003 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 925) hydrogen bonds : angle 4.60492 ( 2688) covalent geometry : bond 0.00264 (22621) covalent geometry : angle 0.63398 (30639) ********************** 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 291 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 212 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8534 (tp40) cc_final: 0.7995 (pm20) REVERT: A 688 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6298 (tt) REVERT: A 770 MET cc_start: 0.7709 (ttm) cc_final: 0.7365 (ttm) REVERT: A 884 MET cc_start: 0.7589 (tpt) cc_final: 0.7266 (tpp) REVERT: A 964 LYS cc_start: 0.8174 (tmmt) cc_final: 0.7851 (pttm) REVERT: B 443 TRP cc_start: 0.6758 (m100) cc_final: 0.5961 (m100) REVERT: B 458 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6306 (ptp) REVERT: B 472 MET cc_start: 0.7254 (mpp) cc_final: 0.6465 (mpp) REVERT: D 122 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5189 (tpp) REVERT: D 425 HIS cc_start: 0.8218 (m170) cc_final: 0.7928 (m90) REVERT: D 487 ARG cc_start: 0.7550 (ptp-170) cc_final: 0.7292 (ptp-170) REVERT: D 565 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: D 668 SER cc_start: 0.8096 (t) cc_final: 0.7802 (p) REVERT: D 854 ASP cc_start: 0.6925 (p0) cc_final: 0.6510 (t0) REVERT: E 443 TRP cc_start: 0.7125 (m100) cc_final: 0.6549 (m100) REVERT: E 567 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7322 (mm) REVERT: F 49 MET cc_start: 0.6780 (mpp) cc_final: 0.6541 (mmt) REVERT: F 108 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6350 (ttm) outliers start: 79 outliers final: 66 residues processed: 270 average time/residue: 0.3130 time to fit residues: 138.0958 Evaluate side-chains 279 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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 324 PHE 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 558 VAL 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 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 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 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL 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 139 HIS 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 317 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 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 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 E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU 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 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 274 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 266 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 323 ASN B 383 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** 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 = 0.4726 r_free = 0.4726 target = 0.180838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.144011 restraints weight = 39087.055| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 3.06 r_work: 0.4170 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22621 Z= 0.141 Angle : 0.649 14.005 30639 Z= 0.320 Chirality : 0.042 0.247 3528 Planarity : 0.004 0.046 3878 Dihedral : 4.755 55.946 2974 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.36 % Allowed : 20.38 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2790 helix: 1.45 (0.16), residues: 1075 sheet: -0.61 (0.22), residues: 561 loop : -1.82 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 525 HIS 0.010 0.001 HIS E 292 PHE 0.013 0.001 PHE D 366 TYR 0.018 0.002 TYR D 247 ARG 0.003 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 925) hydrogen bonds : angle 4.65054 ( 2688) covalent geometry : bond 0.00321 (22621) covalent geometry : angle 0.64908 (30639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15500.30 seconds wall clock time: 271 minutes 16.91 seconds (16276.91 seconds total)