Starting phenix.real_space_refine on Wed Nov 19 22:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tji_8414/11_2025/5tji_8414.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tji_8414/11_2025/5tji_8414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5tji_8414/11_2025/5tji_8414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tji_8414/11_2025/5tji_8414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5tji_8414/11_2025/5tji_8414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tji_8414/11_2025/5tji_8414.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 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 164 5.16 5 C 18048 2.51 5 N 4560 2.21 5 O 4948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 6921 Classifications: {'peptide': 882} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 33, 'TRANS': 848} Chain breaks: 6 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D Time building chain proxies: 6.43, per 1000 atoms: 0.23 Number of scatterers: 27720 At special positions: 0 Unit cell: (152.55, 152.55, 125.55, 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 164 16.00 O 4948 8.00 N 4560 7.00 C 18048 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6656 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 16 sheets defined 55.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 17 through 44 removed outlier: 3.799A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.578A pdb=" N ASP A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 124 removed outlier: 3.876A pdb=" N ILE A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 removed outlier: 3.681A pdb=" N GLN A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 169 through 189 removed outlier: 3.540A pdb=" N PHE A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.574A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.710A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.647A pdb=" N LEU A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 317 removed outlier: 3.711A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.605A pdb=" N ILE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.907A pdb=" N ASN A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 removed outlier: 3.794A pdb=" N GLY A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 removed outlier: 4.033A pdb=" N VAL A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 454 through 460 removed outlier: 4.064A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.640A pdb=" N GLY A 469 " --> pdb=" O TRP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.612A pdb=" N ILE A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 512 through 524 removed outlier: 3.916A pdb=" N MET A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.683A pdb=" N PHE A 535 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.846A pdb=" N LEU A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.801A pdb=" N VAL A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 721 through 726 removed outlier: 4.406A pdb=" N CYS A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 764 Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 781 through 793 removed outlier: 4.317A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 788 " --> pdb=" O TYR A 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 839 through 852 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.662A pdb=" N SER A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 952 Processing helix chain 'A' and resid 956 through 966 removed outlier: 3.969A pdb=" N GLU A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 965 " --> pdb=" O GLN A 961 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.813A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 997 through 1002' Processing helix chain 'A' and resid 1005 through 1016 removed outlier: 3.635A pdb=" N HIS A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 44 removed outlier: 3.799A pdb=" N SER B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 31 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.578A pdb=" N ASP B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 124 removed outlier: 3.876A pdb=" N ILE B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 160 removed outlier: 3.681A pdb=" N GLN B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 169 through 189 removed outlier: 3.540A pdb=" N PHE B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Proline residue: B 180 - end of helix removed outlier: 3.574A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 218 through 249 removed outlier: 3.710A pdb=" N VAL B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.647A pdb=" N LEU B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 317 removed outlier: 3.711A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Proline residue: B 309 - end of helix removed outlier: 3.605A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.907A pdb=" N ASN B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 removed outlier: 3.794A pdb=" N GLY B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 404 removed outlier: 4.033A pdb=" N VAL B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 454 through 460 removed outlier: 4.064A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.640A pdb=" N GLY B 469 " --> pdb=" O TRP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.612A pdb=" N ILE B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 512 through 524 removed outlier: 3.916A pdb=" N MET B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.683A pdb=" N PHE B 535 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 550 removed outlier: 3.846A pdb=" N LEU B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.801A pdb=" N VAL B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 597 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 721 through 726 removed outlier: 4.406A pdb=" N CYS B 725 " --> pdb=" O PRO B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 764 Proline residue: B 762 - end of helix Processing helix chain 'B' and resid 781 through 793 removed outlier: 4.317A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 788 " --> pdb=" O TYR B 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 839 through 852 Processing helix chain 'B' and resid 895 through 901 Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 928 through 940 removed outlier: 3.662A pdb=" N SER B 932 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 952 Processing helix chain 'B' and resid 956 through 966 removed outlier: 3.969A pdb=" N GLU B 960 " --> pdb=" O THR B 956 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 965 " --> pdb=" O GLN B 961 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.813A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 997 through 1002' Processing helix chain 'B' and resid 1005 through 1016 removed outlier: 3.635A pdb=" N HIS B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 44 removed outlier: 3.799A pdb=" N SER C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 31 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.578A pdb=" N ASP C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 124 removed outlier: 3.876A pdb=" N ILE C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 160 removed outlier: 3.681A pdb=" N GLN C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 169 through 189 removed outlier: 3.540A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 3.574A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 218 through 249 removed outlier: 3.710A pdb=" N VAL C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 275 removed outlier: 3.647A pdb=" N LEU C 267 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 317 removed outlier: 3.711A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Proline residue: C 309 - end of helix removed outlier: 3.605A pdb=" N ILE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.907A pdb=" N ASN C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 removed outlier: 3.794A pdb=" N GLY C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 404 removed outlier: 4.033A pdb=" N VAL C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 454 through 460 removed outlier: 4.064A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.640A pdb=" N GLY C 469 " --> pdb=" O TRP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.612A pdb=" N ILE C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 512 through 524 removed outlier: 3.916A pdb=" N MET C 524 " --> pdb=" O ARG C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.683A pdb=" N PHE C 535 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 550 removed outlier: 3.846A pdb=" N LEU C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.801A pdb=" N VAL C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 721 through 726 removed outlier: 4.406A pdb=" N CYS C 725 " --> pdb=" O PRO C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 764 Proline residue: C 762 - end of helix Processing helix chain 'C' and resid 781 through 793 removed outlier: 4.317A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 788 " --> pdb=" O TYR C 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 815 Processing helix chain 'C' and resid 839 through 852 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 928 through 940 removed outlier: 3.662A pdb=" N SER C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 936 " --> pdb=" O SER C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 952 Processing helix chain 'C' and resid 956 through 966 removed outlier: 3.969A pdb=" N GLU C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 965 " --> pdb=" O GLN C 961 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.813A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN C1002 " --> pdb=" O ALA C 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 997 through 1002' Processing helix chain 'C' and resid 1005 through 1016 removed outlier: 3.635A pdb=" N HIS C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 44 removed outlier: 3.799A pdb=" N SER D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 31 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 32 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.578A pdb=" N ASP D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 124 removed outlier: 3.876A pdb=" N ILE D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 160 removed outlier: 3.681A pdb=" N GLN D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 169 through 189 removed outlier: 3.540A pdb=" N PHE D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 3.574A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 218 through 249 removed outlier: 3.710A pdb=" N VAL D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 247 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 275 removed outlier: 3.647A pdb=" N LEU D 267 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR D 268 " --> pdb=" O TRP D 264 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 317 removed outlier: 3.711A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) Proline residue: D 309 - end of helix removed outlier: 3.605A pdb=" N ILE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.907A pdb=" N ASN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.794A pdb=" N GLY D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 404 removed outlier: 4.033A pdb=" N VAL D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 454 through 460 removed outlier: 4.064A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 459 " --> pdb=" O LYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.640A pdb=" N GLY D 469 " --> pdb=" O TRP D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.612A pdb=" N ILE D 483 " --> pdb=" O LYS D 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 512 through 524 removed outlier: 3.916A pdb=" N MET D 524 " --> pdb=" O ARG D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.683A pdb=" N PHE D 535 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 550 removed outlier: 3.846A pdb=" N LEU D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.801A pdb=" N VAL D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 597 " --> pdb=" O ALA D 593 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 721 through 726 removed outlier: 4.406A pdb=" N CYS D 725 " --> pdb=" O PRO D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 764 Proline residue: D 762 - end of helix Processing helix chain 'D' and resid 781 through 793 removed outlier: 4.317A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 788 " --> pdb=" O TYR D 784 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 815 Processing helix chain 'D' and resid 839 through 852 Processing helix chain 'D' and resid 895 through 901 Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 928 through 940 removed outlier: 3.662A pdb=" N SER D 932 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET D 934 " --> pdb=" O LEU D 930 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 952 Processing helix chain 'D' and resid 956 through 966 removed outlier: 3.969A pdb=" N GLU D 960 " --> pdb=" O THR D 956 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 965 " --> pdb=" O GLN D 961 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY D 966 " --> pdb=" O ILE D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.813A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN D1002 " --> pdb=" O ALA D 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 997 through 1002' Processing helix chain 'D' and resid 1005 through 1016 removed outlier: 3.635A pdb=" N HIS D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 387 through 391 removed outlier: 3.650A pdb=" N HIS A 368 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS A 411 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLN A 448 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL A 413 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 445 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 473 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 447 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.935A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 589 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 554 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 571 " --> pdb=" O ILE A 558 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 801 through 802 removed outlier: 7.578A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 742 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 825 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS A 744 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS A 822 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU A 891 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 824 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG A 986 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 387 through 391 removed outlier: 3.650A pdb=" N HIS B 368 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS B 411 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLN B 448 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 413 " --> pdb=" O GLN B 448 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 445 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL B 473 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B 447 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.935A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 589 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 554 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 571 " --> pdb=" O ILE B 558 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 801 through 802 removed outlier: 7.578A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 742 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 825 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS B 744 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS B 822 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU B 891 " --> pdb=" O CYS B 822 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE B 824 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG B 986 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 387 through 391 removed outlier: 3.650A pdb=" N HIS C 368 " --> pdb=" O PHE C 390 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS C 411 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLN C 448 " --> pdb=" O CYS C 411 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL C 413 " --> pdb=" O GLN C 448 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL C 445 " --> pdb=" O ASP C 471 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL C 473 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 447 " --> pdb=" O VAL C 473 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.935A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 589 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 554 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 571 " --> pdb=" O ILE C 558 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 801 through 802 removed outlier: 7.578A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 742 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 825 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS C 744 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS C 822 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU C 891 " --> pdb=" O CYS C 822 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE C 824 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG C 986 " --> pdb=" O THR C1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 387 through 391 removed outlier: 3.650A pdb=" N HIS D 368 " --> pdb=" O PHE D 390 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS D 411 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLN D 448 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL D 413 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL D 445 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL D 473 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 447 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.935A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 589 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 554 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 571 " --> pdb=" O ILE D 558 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 801 through 802 removed outlier: 7.578A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 742 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL D 825 " --> pdb=" O VAL D 742 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS D 744 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS D 822 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU D 891 " --> pdb=" O CYS D 822 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 824 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.519A pdb=" N ARG D 986 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8624 1.34 - 1.46: 3808 1.46 - 1.58: 15700 1.58 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 28380 Sorted by residual: bond pdb=" CA ILE B 308 " pdb=" CB ILE B 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA ILE D 308 " pdb=" CB ILE D 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA ILE C 308 " pdb=" CB ILE C 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA ILE A 308 " pdb=" CB ILE A 308 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.35e+01 bond pdb=" CA PRO D 180 " pdb=" C PRO D 180 " ideal model delta sigma weight residual 1.517 1.543 -0.026 9.30e-03 1.16e+04 7.87e+00 ... (remaining 28375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 31284 1.22 - 2.44: 6388 2.44 - 3.66: 760 3.66 - 4.89: 116 4.89 - 6.11: 20 Bond angle restraints: 38568 Sorted by residual: angle pdb=" N VAL D 215 " pdb=" CA VAL D 215 " pdb=" C VAL D 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N VAL A 215 " pdb=" CA VAL A 215 " pdb=" C VAL A 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N VAL C 215 " pdb=" CA VAL C 215 " pdb=" C VAL C 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N VAL B 215 " pdb=" CA VAL B 215 " pdb=" C VAL B 215 " ideal model delta sigma weight residual 111.45 106.11 5.34 9.30e-01 1.16e+00 3.30e+01 angle pdb=" N PRO A 180 " pdb=" CA PRO A 180 " pdb=" C PRO A 180 " ideal model delta sigma weight residual 110.70 116.81 -6.11 1.22e+00 6.72e-01 2.51e+01 ... (remaining 38563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 15172 14.92 - 29.84: 1092 29.84 - 44.76: 268 44.76 - 59.68: 92 59.68 - 74.59: 4 Dihedral angle restraints: 16628 sinusoidal: 6336 harmonic: 10292 Sorted by residual: dihedral pdb=" CA ARG B1026 " pdb=" C ARG B1026 " pdb=" N PHE B1027 " pdb=" CA PHE B1027 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ARG D1026 " pdb=" C ARG D1026 " pdb=" N PHE D1027 " pdb=" CA PHE D1027 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ARG A1026 " pdb=" C ARG A1026 " pdb=" N PHE A1027 " pdb=" CA PHE A1027 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 16625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2716 0.043 - 0.087: 1128 0.087 - 0.130: 380 0.130 - 0.173: 164 0.173 - 0.217: 28 Chirality restraints: 4416 Sorted by residual: chirality pdb=" CA ILE C1044 " pdb=" N ILE C1044 " pdb=" C ILE C1044 " pdb=" CB ILE C1044 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A1044 " pdb=" N ILE A1044 " pdb=" C ILE A1044 " pdb=" CB ILE A1044 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B1044 " pdb=" N ILE B1044 " pdb=" C ILE B1044 " pdb=" CB ILE B1044 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4413 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 308 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO D 309 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 309 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 309 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 308 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 309 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 308 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 309 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.022 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 11380 2.97 - 3.45: 27232 3.45 - 3.93: 42564 3.93 - 4.42: 47466 4.42 - 4.90: 81778 Nonbonded interactions: 210420 Sorted by model distance: nonbonded pdb=" O PRO B 490 " pdb=" OH TYR B1060 " model vdw 2.483 3.040 nonbonded pdb=" O PRO A 490 " pdb=" OH TYR A1060 " model vdw 2.483 3.040 nonbonded pdb=" O PRO D 490 " pdb=" OH TYR D1060 " model vdw 2.483 3.040 nonbonded pdb=" O PRO C 490 " pdb=" OH TYR C1060 " model vdw 2.483 3.040 nonbonded pdb=" O VAL D 929 " pdb=" OG SER D 932 " model vdw 2.486 3.040 ... (remaining 210415 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.007 0.037 28380 Z= 0.471 Angle : 0.985 6.108 38568 Z= 0.683 Chirality : 0.058 0.217 4416 Planarity : 0.003 0.039 4856 Dihedral : 11.752 74.594 9972 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.99 % Favored : 93.78 % Rotamer: Outliers : 0.41 % Allowed : 2.17 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.12), residues: 3472 helix: -1.73 (0.10), residues: 1572 sheet: -3.02 (0.20), residues: 456 loop : -1.88 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 984 TYR 0.011 0.001 TYR D 914 PHE 0.014 0.001 PHE A 482 TRP 0.010 0.001 TRP B 789 HIS 0.002 0.001 HIS B 453 Details of bonding type rmsd covalent geometry : bond 0.00667 (28380) covalent geometry : angle 0.98484 (38568) hydrogen bonds : bond 0.30568 ( 1164) hydrogen bonds : angle 8.32033 ( 3264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9852 (tpp) cc_final: 0.9519 (mmm) REVERT: A 496 MET cc_start: 0.9899 (mmm) cc_final: 0.9598 (mmm) REVERT: A 502 MET cc_start: 0.9189 (tpp) cc_final: 0.8252 (ttm) REVERT: A 519 MET cc_start: 0.9619 (mmm) cc_final: 0.9405 (mmm) REVERT: A 761 MET cc_start: 0.9933 (ttm) cc_final: 0.9583 (tpp) REVERT: A 934 MET cc_start: 0.9616 (mmm) cc_final: 0.9003 (mmm) REVERT: B 431 MET cc_start: 0.9852 (tpp) cc_final: 0.9519 (mmm) REVERT: B 496 MET cc_start: 0.9899 (mmm) cc_final: 0.9599 (mmm) REVERT: B 502 MET cc_start: 0.9188 (tpp) cc_final: 0.8252 (ttm) REVERT: B 519 MET cc_start: 0.9617 (mmm) cc_final: 0.9406 (mmm) REVERT: B 761 MET cc_start: 0.9933 (ttm) cc_final: 0.9583 (tpp) REVERT: B 934 MET cc_start: 0.9618 (mmm) cc_final: 0.9004 (mmm) REVERT: C 431 MET cc_start: 0.9852 (tpp) cc_final: 0.9519 (mmm) REVERT: C 496 MET cc_start: 0.9899 (mmm) cc_final: 0.9598 (mmm) REVERT: C 502 MET cc_start: 0.9189 (tpp) cc_final: 0.8252 (ttm) REVERT: C 519 MET cc_start: 0.9618 (mmm) cc_final: 0.9405 (mmm) REVERT: C 761 MET cc_start: 0.9933 (ttm) cc_final: 0.9583 (tpp) REVERT: C 934 MET cc_start: 0.9617 (mmm) cc_final: 0.9004 (mmm) REVERT: D 431 MET cc_start: 0.9852 (tpp) cc_final: 0.9519 (mmm) REVERT: D 496 MET cc_start: 0.9899 (mmm) cc_final: 0.9598 (mmm) REVERT: D 502 MET cc_start: 0.9189 (tpp) cc_final: 0.8253 (ttm) REVERT: D 519 MET cc_start: 0.9618 (mmm) cc_final: 0.9405 (mmm) REVERT: D 761 MET cc_start: 0.9933 (ttm) cc_final: 0.9583 (tpp) REVERT: D 934 MET cc_start: 0.9617 (mmm) cc_final: 0.9004 (mmm) outliers start: 12 outliers final: 0 residues processed: 120 average time/residue: 0.2021 time to fit residues: 38.8013 Evaluate side-chains 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 453 HIS A 454 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS B 451 GLN B 453 HIS B 454 ASN ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 HIS C 451 GLN C 453 HIS C 454 ASN ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 HIS D 451 GLN D 453 HIS D 454 ASN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.029547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.023481 restraints weight = 462072.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.023700 restraints weight = 367820.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 100)---------------| | r_work = 0.3123 r_free = 0.3123 target = 0.024046 restraints weight = 289706.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.024146 restraints weight = 222886.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.024245 restraints weight = 172989.940| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28380 Z= 0.170 Angle : 0.574 8.575 38568 Z= 0.292 Chirality : 0.039 0.140 4416 Planarity : 0.004 0.037 4856 Dihedral : 4.281 18.220 3812 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.68 % Allowed : 3.46 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3472 helix: 0.02 (0.12), residues: 1804 sheet: -2.46 (0.21), residues: 448 loop : -1.39 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 984 TYR 0.013 0.002 TYR D 527 PHE 0.033 0.002 PHE B 241 TRP 0.010 0.001 TRP B 514 HIS 0.004 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00341 (28380) covalent geometry : angle 0.57436 (38568) hydrogen bonds : bond 0.04392 ( 1164) hydrogen bonds : angle 4.37205 ( 3264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.9620 (mmm) cc_final: 0.9405 (mtm) REVERT: A 502 MET cc_start: 0.9206 (tpp) cc_final: 0.8651 (ttm) REVERT: A 524 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.9087 (mmm) REVERT: A 934 MET cc_start: 0.9632 (mmm) cc_final: 0.9035 (mmm) REVERT: B 496 MET cc_start: 0.9685 (mmm) cc_final: 0.9436 (mtm) REVERT: B 502 MET cc_start: 0.9222 (tpp) cc_final: 0.8620 (ttm) REVERT: B 524 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9076 (mmm) REVERT: B 761 MET cc_start: 0.9711 (ttm) cc_final: 0.9396 (tmm) REVERT: B 934 MET cc_start: 0.9661 (mmm) cc_final: 0.9054 (mmm) REVERT: C 496 MET cc_start: 0.9689 (mmm) cc_final: 0.9443 (mtm) REVERT: C 502 MET cc_start: 0.9227 (tpp) cc_final: 0.8643 (ttm) REVERT: C 524 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9071 (mmm) REVERT: C 761 MET cc_start: 0.9663 (ttm) cc_final: 0.9387 (tmm) REVERT: C 934 MET cc_start: 0.9660 (mmm) cc_final: 0.9044 (mmm) REVERT: D 496 MET cc_start: 0.9675 (mmm) cc_final: 0.9437 (mtm) REVERT: D 502 MET cc_start: 0.9255 (tpp) cc_final: 0.8634 (ttm) REVERT: D 524 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (mmm) REVERT: D 761 MET cc_start: 0.9560 (ttm) cc_final: 0.9332 (tmm) REVERT: D 934 MET cc_start: 0.9662 (mmm) cc_final: 0.9052 (mmm) outliers start: 20 outliers final: 0 residues processed: 100 average time/residue: 0.1935 time to fit residues: 32.1200 Evaluate side-chains 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain D residue 524 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 133 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.029285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.023069 restraints weight = 461043.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.023069 restraints weight = 331077.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.023069 restraints weight = 331077.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.023069 restraints weight = 331077.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.023069 restraints weight = 331077.886| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28380 Z= 0.170 Angle : 0.544 6.467 38568 Z= 0.275 Chirality : 0.038 0.178 4416 Planarity : 0.004 0.035 4856 Dihedral : 3.970 16.153 3812 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.54 % Allowed : 4.21 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3472 helix: 0.78 (0.13), residues: 1816 sheet: -1.90 (0.23), residues: 440 loop : -1.02 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 598 TYR 0.017 0.001 TYR A 914 PHE 0.025 0.001 PHE C 241 TRP 0.010 0.001 TRP D 789 HIS 0.005 0.001 HIS D1016 Details of bonding type rmsd covalent geometry : bond 0.00342 (28380) covalent geometry : angle 0.54403 (38568) hydrogen bonds : bond 0.03342 ( 1164) hydrogen bonds : angle 4.12360 ( 3264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9781 (mmm) cc_final: 0.9559 (mtt) REVERT: A 496 MET cc_start: 0.9773 (mmm) cc_final: 0.9508 (mtm) REVERT: A 502 MET cc_start: 0.9597 (tpp) cc_final: 0.8851 (mtp) REVERT: A 524 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.9170 (mmm) REVERT: A 713 MET cc_start: 0.8336 (mmm) cc_final: 0.7992 (tpp) REVERT: A 821 MET cc_start: 0.9564 (tpt) cc_final: 0.9078 (tpt) REVERT: A 852 MET cc_start: 0.9293 (mmm) cc_final: 0.8743 (mmm) REVERT: A 915 MET cc_start: 0.9673 (mmm) cc_final: 0.9451 (mmm) REVERT: A 934 MET cc_start: 0.9818 (mmm) cc_final: 0.9244 (mmm) REVERT: B 431 MET cc_start: 0.9773 (mmm) cc_final: 0.9556 (mtt) REVERT: B 496 MET cc_start: 0.9756 (mmm) cc_final: 0.9504 (mtm) REVERT: B 502 MET cc_start: 0.9550 (tpp) cc_final: 0.8851 (mtp) REVERT: B 524 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9158 (mmm) REVERT: B 713 MET cc_start: 0.8343 (mmm) cc_final: 0.7974 (tpp) REVERT: B 761 MET cc_start: 0.9449 (ttm) cc_final: 0.9150 (tpp) REVERT: B 821 MET cc_start: 0.9588 (tpt) cc_final: 0.9103 (tpt) REVERT: B 852 MET cc_start: 0.9313 (mmm) cc_final: 0.8757 (mmm) REVERT: B 915 MET cc_start: 0.9704 (mmm) cc_final: 0.9485 (mmm) REVERT: B 934 MET cc_start: 0.9808 (mmm) cc_final: 0.9222 (mmm) REVERT: C 431 MET cc_start: 0.9784 (mmm) cc_final: 0.9556 (mtt) REVERT: C 496 MET cc_start: 0.9751 (mmm) cc_final: 0.9502 (mtm) REVERT: C 502 MET cc_start: 0.9563 (tpp) cc_final: 0.8843 (mtp) REVERT: C 524 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9163 (mmm) REVERT: C 713 MET cc_start: 0.8402 (mmm) cc_final: 0.7981 (tpp) REVERT: C 761 MET cc_start: 0.9403 (ttm) cc_final: 0.9128 (tpp) REVERT: C 821 MET cc_start: 0.9559 (tpt) cc_final: 0.9066 (tpt) REVERT: C 852 MET cc_start: 0.9267 (mmm) cc_final: 0.8720 (mmm) REVERT: C 915 MET cc_start: 0.9691 (mmm) cc_final: 0.9465 (mmm) REVERT: C 934 MET cc_start: 0.9813 (mmm) cc_final: 0.9237 (mmm) REVERT: D 431 MET cc_start: 0.9771 (mmm) cc_final: 0.9553 (mtt) REVERT: D 496 MET cc_start: 0.9764 (mmm) cc_final: 0.9523 (mtm) REVERT: D 502 MET cc_start: 0.9596 (tpp) cc_final: 0.8871 (mtp) REVERT: D 524 MET cc_start: 0.9545 (OUTLIER) cc_final: 0.9177 (mmm) REVERT: D 713 MET cc_start: 0.8340 (mmm) cc_final: 0.8042 (tpp) REVERT: D 761 MET cc_start: 0.9383 (ttm) cc_final: 0.9146 (tpp) REVERT: D 821 MET cc_start: 0.9595 (tpt) cc_final: 0.9121 (tpt) REVERT: D 852 MET cc_start: 0.9250 (mmm) cc_final: 0.8729 (mmm) REVERT: D 915 MET cc_start: 0.9693 (mmm) cc_final: 0.9472 (mmm) REVERT: D 934 MET cc_start: 0.9810 (mmm) cc_final: 0.9225 (mmm) outliers start: 16 outliers final: 0 residues processed: 104 average time/residue: 0.1886 time to fit residues: 32.4830 Evaluate side-chains 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain D residue 524 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 146 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 351 optimal weight: 30.0000 chunk 344 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 279 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 185 optimal weight: 40.0000 chunk 340 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS A 781 ASN ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 HIS B 781 ASN ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 ASN ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 HIS D 781 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.029245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.022764 restraints weight = 455645.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.022863 restraints weight = 394397.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.022863 restraints weight = 325759.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.022862 restraints weight = 325760.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.023024 restraints weight = 325967.858| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28380 Z= 0.157 Angle : 0.513 6.971 38568 Z= 0.259 Chirality : 0.037 0.123 4416 Planarity : 0.003 0.031 4856 Dihedral : 3.824 14.443 3812 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.68 % Allowed : 4.61 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3472 helix: 1.10 (0.13), residues: 1828 sheet: -1.32 (0.25), residues: 396 loop : -0.69 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 598 TYR 0.010 0.001 TYR B 418 PHE 0.019 0.001 PHE C 241 TRP 0.011 0.002 TRP C 192 HIS 0.004 0.001 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00319 (28380) covalent geometry : angle 0.51258 (38568) hydrogen bonds : bond 0.02792 ( 1164) hydrogen bonds : angle 3.91903 ( 3264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9775 (mmm) cc_final: 0.9237 (mmm) REVERT: A 496 MET cc_start: 0.9749 (mmm) cc_final: 0.9500 (mtm) REVERT: A 502 MET cc_start: 0.9582 (tpp) cc_final: 0.8883 (mtp) REVERT: A 524 MET cc_start: 0.9513 (OUTLIER) cc_final: 0.9150 (mmm) REVERT: A 852 MET cc_start: 0.9275 (mmm) cc_final: 0.8805 (mmm) REVERT: A 934 MET cc_start: 0.9822 (mmm) cc_final: 0.9294 (mmm) REVERT: B 431 MET cc_start: 0.9776 (mmm) cc_final: 0.9225 (mmm) REVERT: B 496 MET cc_start: 0.9758 (mmm) cc_final: 0.9552 (mtm) REVERT: B 502 MET cc_start: 0.9562 (tpp) cc_final: 0.8844 (mtp) REVERT: B 524 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9178 (mmm) REVERT: B 713 MET cc_start: 0.9277 (mmm) cc_final: 0.8413 (tpp) REVERT: B 761 MET cc_start: 0.9672 (ttm) cc_final: 0.9026 (tpp) REVERT: B 777 ILE cc_start: 0.9785 (OUTLIER) cc_final: 0.9582 (tp) REVERT: B 852 MET cc_start: 0.9281 (mmm) cc_final: 0.8802 (mmm) REVERT: B 934 MET cc_start: 0.9814 (mmm) cc_final: 0.9265 (mmm) REVERT: C 431 MET cc_start: 0.9780 (mmm) cc_final: 0.9239 (mmm) REVERT: C 496 MET cc_start: 0.9767 (mmm) cc_final: 0.9559 (mtm) REVERT: C 502 MET cc_start: 0.9561 (tpp) cc_final: 0.8838 (mtp) REVERT: C 524 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9158 (mmm) REVERT: C 713 MET cc_start: 0.9297 (mmm) cc_final: 0.8403 (tpp) REVERT: C 761 MET cc_start: 0.9678 (ttm) cc_final: 0.9054 (tpp) REVERT: C 777 ILE cc_start: 0.9808 (OUTLIER) cc_final: 0.9579 (tp) REVERT: C 852 MET cc_start: 0.9239 (mmm) cc_final: 0.8788 (mmm) REVERT: C 934 MET cc_start: 0.9830 (mmm) cc_final: 0.9297 (mmm) REVERT: D 431 MET cc_start: 0.9774 (mmm) cc_final: 0.9232 (mmm) REVERT: D 496 MET cc_start: 0.9741 (mmm) cc_final: 0.9524 (mtm) REVERT: D 502 MET cc_start: 0.9574 (tpp) cc_final: 0.8854 (mtp) REVERT: D 524 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9151 (mmm) REVERT: D 713 MET cc_start: 0.9250 (mmm) cc_final: 0.8405 (tpp) REVERT: D 761 MET cc_start: 0.9622 (ttm) cc_final: 0.9002 (tpp) REVERT: D 777 ILE cc_start: 0.9781 (OUTLIER) cc_final: 0.9570 (tp) REVERT: D 852 MET cc_start: 0.9293 (mmm) cc_final: 0.8806 (mmm) REVERT: D 934 MET cc_start: 0.9818 (mmm) cc_final: 0.9273 (mmm) outliers start: 20 outliers final: 0 residues processed: 108 average time/residue: 0.1878 time to fit residues: 33.9159 Evaluate side-chains 99 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 777 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 348 optimal weight: 30.0000 chunk 287 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 198 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.029323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.022771 restraints weight = 456481.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.022771 restraints weight = 393426.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.022771 restraints weight = 393353.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.022771 restraints weight = 393311.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.022771 restraints weight = 393311.976| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28380 Z= 0.146 Angle : 0.530 11.048 38568 Z= 0.261 Chirality : 0.037 0.160 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.808 17.766 3812 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.64 % Allowed : 5.09 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3472 helix: 1.28 (0.13), residues: 1820 sheet: -1.01 (0.26), residues: 396 loop : -0.61 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 970 TYR 0.013 0.001 TYR C 914 PHE 0.016 0.001 PHE A 241 TRP 0.007 0.001 TRP A 514 HIS 0.004 0.001 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00299 (28380) covalent geometry : angle 0.53020 (38568) hydrogen bonds : bond 0.02512 ( 1164) hydrogen bonds : angle 3.90641 ( 3264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9788 (mmm) cc_final: 0.9254 (mmm) REVERT: A 496 MET cc_start: 0.9792 (mmm) cc_final: 0.9569 (mtm) REVERT: A 502 MET cc_start: 0.9660 (tpp) cc_final: 0.8965 (mtp) REVERT: A 524 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9204 (tpp) REVERT: A 713 MET cc_start: 0.7976 (tpp) cc_final: 0.7421 (tpp) REVERT: A 852 MET cc_start: 0.9217 (mmm) cc_final: 0.8796 (mmm) REVERT: A 934 MET cc_start: 0.9852 (mmm) cc_final: 0.9336 (mmm) REVERT: B 431 MET cc_start: 0.9770 (mmm) cc_final: 0.9224 (mmm) REVERT: B 496 MET cc_start: 0.9766 (mmm) cc_final: 0.9539 (mtm) REVERT: B 502 MET cc_start: 0.9635 (tpp) cc_final: 0.8955 (mtp) REVERT: B 524 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.9207 (tpp) REVERT: B 713 MET cc_start: 0.8737 (mmm) cc_final: 0.8209 (tpp) REVERT: B 761 MET cc_start: 0.9320 (ttm) cc_final: 0.8839 (tpp) REVERT: B 777 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9522 (tp) REVERT: B 852 MET cc_start: 0.9255 (mmm) cc_final: 0.8812 (mmm) REVERT: B 934 MET cc_start: 0.9850 (mmm) cc_final: 0.9315 (mmm) REVERT: C 431 MET cc_start: 0.9777 (mmm) cc_final: 0.9247 (mmm) REVERT: C 496 MET cc_start: 0.9771 (mmm) cc_final: 0.9539 (mtm) REVERT: C 502 MET cc_start: 0.9644 (tpp) cc_final: 0.8974 (mtp) REVERT: C 524 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9189 (tpp) REVERT: C 713 MET cc_start: 0.8655 (mmm) cc_final: 0.8215 (tpp) REVERT: C 761 MET cc_start: 0.9382 (ttm) cc_final: 0.8985 (tpp) REVERT: C 777 ILE cc_start: 0.9729 (OUTLIER) cc_final: 0.9506 (tp) REVERT: C 852 MET cc_start: 0.9222 (mmm) cc_final: 0.8789 (mmm) REVERT: C 934 MET cc_start: 0.9845 (mmm) cc_final: 0.9322 (mmm) REVERT: D 431 MET cc_start: 0.9785 (mmm) cc_final: 0.9240 (mmm) REVERT: D 496 MET cc_start: 0.9788 (mmm) cc_final: 0.9564 (mtm) REVERT: D 502 MET cc_start: 0.9649 (tpp) cc_final: 0.8952 (mtp) REVERT: D 524 MET cc_start: 0.9511 (OUTLIER) cc_final: 0.9237 (tpp) REVERT: D 713 MET cc_start: 0.8830 (mmm) cc_final: 0.8274 (tpp) REVERT: D 761 MET cc_start: 0.9332 (ttm) cc_final: 0.8872 (tpp) REVERT: D 777 ILE cc_start: 0.9726 (OUTLIER) cc_final: 0.9506 (tp) REVERT: D 852 MET cc_start: 0.9257 (mmm) cc_final: 0.8814 (mmm) REVERT: D 934 MET cc_start: 0.9853 (mmm) cc_final: 0.9319 (mmm) outliers start: 19 outliers final: 8 residues processed: 99 average time/residue: 0.1908 time to fit residues: 31.3874 Evaluate side-chains 107 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 821 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 821 MET Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 777 ILE Chi-restraints excluded: chain D residue 821 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 124 optimal weight: 0.4980 chunk 150 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 268 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 110 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.029172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022714 restraints weight = 457819.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022714 restraints weight = 400143.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022714 restraints weight = 400143.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022714 restraints weight = 400143.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022714 restraints weight = 400143.099| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 28380 Z= 0.114 Angle : 0.490 8.488 38568 Z= 0.245 Chirality : 0.037 0.134 4416 Planarity : 0.003 0.028 4856 Dihedral : 3.723 21.510 3812 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.51 % Allowed : 6.14 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3472 helix: 1.43 (0.13), residues: 1808 sheet: -0.76 (0.27), residues: 392 loop : -0.60 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 614 TYR 0.008 0.001 TYR C 914 PHE 0.014 0.001 PHE D 241 TRP 0.006 0.001 TRP C 16 HIS 0.003 0.001 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00237 (28380) covalent geometry : angle 0.48982 (38568) hydrogen bonds : bond 0.02405 ( 1164) hydrogen bonds : angle 3.83500 ( 3264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9781 (mmm) cc_final: 0.9218 (mmm) REVERT: A 496 MET cc_start: 0.9792 (mmm) cc_final: 0.9574 (mtm) REVERT: A 502 MET cc_start: 0.9662 (tpp) cc_final: 0.9058 (mtp) REVERT: A 524 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.9203 (tpp) REVERT: A 713 MET cc_start: 0.8143 (tpp) cc_final: 0.7715 (tpp) REVERT: A 852 MET cc_start: 0.9266 (mmm) cc_final: 0.8815 (mmm) REVERT: A 915 MET cc_start: 0.9422 (mmm) cc_final: 0.9126 (mmm) REVERT: A 934 MET cc_start: 0.9859 (mmm) cc_final: 0.9364 (mmm) REVERT: B 431 MET cc_start: 0.9762 (mmm) cc_final: 0.9187 (mmm) REVERT: B 496 MET cc_start: 0.9773 (mmm) cc_final: 0.9561 (mtm) REVERT: B 502 MET cc_start: 0.9636 (tpp) cc_final: 0.9046 (mtp) REVERT: B 524 MET cc_start: 0.9492 (OUTLIER) cc_final: 0.9193 (tpp) REVERT: B 713 MET cc_start: 0.8696 (mmm) cc_final: 0.8055 (tpp) REVERT: B 761 MET cc_start: 0.9340 (ttm) cc_final: 0.8917 (tpp) REVERT: B 852 MET cc_start: 0.9223 (mmm) cc_final: 0.8784 (mmm) REVERT: B 915 MET cc_start: 0.9459 (mmm) cc_final: 0.9164 (mmm) REVERT: B 934 MET cc_start: 0.9853 (mmm) cc_final: 0.9336 (mmm) REVERT: C 431 MET cc_start: 0.9769 (mmm) cc_final: 0.9206 (mmm) REVERT: C 496 MET cc_start: 0.9774 (mmm) cc_final: 0.9564 (mtm) REVERT: C 502 MET cc_start: 0.9643 (tpp) cc_final: 0.9054 (mtp) REVERT: C 524 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9183 (tpp) REVERT: C 713 MET cc_start: 0.8524 (mmm) cc_final: 0.8110 (tpp) REVERT: C 761 MET cc_start: 0.9407 (ttm) cc_final: 0.8992 (tpp) REVERT: C 777 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9507 (tp) REVERT: C 852 MET cc_start: 0.9204 (mmm) cc_final: 0.8763 (mmm) REVERT: C 915 MET cc_start: 0.9428 (mmm) cc_final: 0.9125 (mmm) REVERT: C 934 MET cc_start: 0.9847 (mmm) cc_final: 0.9341 (mmm) REVERT: D 431 MET cc_start: 0.9780 (mmm) cc_final: 0.9198 (mmm) REVERT: D 496 MET cc_start: 0.9784 (mmm) cc_final: 0.9577 (mtm) REVERT: D 502 MET cc_start: 0.9642 (tpp) cc_final: 0.9038 (mtp) REVERT: D 524 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9233 (tpp) REVERT: D 713 MET cc_start: 0.8781 (mmm) cc_final: 0.8096 (tpp) REVERT: D 761 MET cc_start: 0.9329 (ttm) cc_final: 0.8939 (tpp) REVERT: D 852 MET cc_start: 0.9231 (mmm) cc_final: 0.8812 (mmm) REVERT: D 915 MET cc_start: 0.9453 (mmm) cc_final: 0.9158 (mmm) REVERT: D 934 MET cc_start: 0.9859 (mmm) cc_final: 0.9357 (mmm) outliers start: 15 outliers final: 4 residues processed: 99 average time/residue: 0.1888 time to fit residues: 31.3252 Evaluate side-chains 101 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 524 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 231 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.029128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022621 restraints weight = 457338.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022625 restraints weight = 393020.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022625 restraints weight = 388782.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022625 restraints weight = 388438.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.022625 restraints weight = 388438.729| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28380 Z= 0.125 Angle : 0.511 9.285 38568 Z= 0.257 Chirality : 0.037 0.223 4416 Planarity : 0.003 0.028 4856 Dihedral : 3.671 19.819 3812 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.75 % Allowed : 5.80 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3472 helix: 1.54 (0.13), residues: 1800 sheet: -0.61 (0.26), residues: 392 loop : -0.46 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 984 TYR 0.008 0.001 TYR A 389 PHE 0.013 0.001 PHE C 241 TRP 0.007 0.001 TRP A 514 HIS 0.003 0.001 HIS C 740 Details of bonding type rmsd covalent geometry : bond 0.00260 (28380) covalent geometry : angle 0.51096 (38568) hydrogen bonds : bond 0.02486 ( 1164) hydrogen bonds : angle 3.90515 ( 3264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9781 (mmm) cc_final: 0.9198 (mmm) REVERT: A 496 MET cc_start: 0.9793 (mmm) cc_final: 0.9546 (mmm) REVERT: A 502 MET cc_start: 0.9646 (tpp) cc_final: 0.9026 (mtp) REVERT: A 524 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.9241 (tpp) REVERT: A 713 MET cc_start: 0.8201 (tpp) cc_final: 0.7674 (tpp) REVERT: A 852 MET cc_start: 0.9243 (mmm) cc_final: 0.8869 (mmm) REVERT: A 915 MET cc_start: 0.9493 (mmm) cc_final: 0.9175 (mmm) REVERT: A 934 MET cc_start: 0.9864 (mmm) cc_final: 0.9396 (mmm) REVERT: B 431 MET cc_start: 0.9770 (mmm) cc_final: 0.9189 (mmm) REVERT: B 496 MET cc_start: 0.9771 (mmm) cc_final: 0.9555 (mtm) REVERT: B 502 MET cc_start: 0.9640 (tpp) cc_final: 0.9031 (mtp) REVERT: B 524 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9230 (tpp) REVERT: B 713 MET cc_start: 0.8606 (mmm) cc_final: 0.8289 (tpp) REVERT: B 761 MET cc_start: 0.9286 (ttm) cc_final: 0.8945 (tpp) REVERT: B 852 MET cc_start: 0.9247 (mmm) cc_final: 0.8853 (mmm) REVERT: B 915 MET cc_start: 0.9517 (mmm) cc_final: 0.9199 (mmm) REVERT: B 934 MET cc_start: 0.9859 (mmm) cc_final: 0.9365 (mmm) REVERT: C 431 MET cc_start: 0.9772 (mmm) cc_final: 0.9198 (mmm) REVERT: C 496 MET cc_start: 0.9766 (mmm) cc_final: 0.9565 (mtm) REVERT: C 502 MET cc_start: 0.9649 (tpp) cc_final: 0.9028 (mtp) REVERT: C 524 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.9210 (tpp) REVERT: C 713 MET cc_start: 0.8543 (mmm) cc_final: 0.8271 (tpp) REVERT: C 761 MET cc_start: 0.9361 (ttm) cc_final: 0.9018 (tpp) REVERT: C 777 ILE cc_start: 0.9702 (OUTLIER) cc_final: 0.9500 (tp) REVERT: C 852 MET cc_start: 0.9262 (mmm) cc_final: 0.8861 (mmm) REVERT: C 915 MET cc_start: 0.9496 (mmm) cc_final: 0.9171 (mmm) REVERT: C 934 MET cc_start: 0.9859 (mmm) cc_final: 0.9373 (mmm) REVERT: D 431 MET cc_start: 0.9774 (mmm) cc_final: 0.9178 (mmm) REVERT: D 502 MET cc_start: 0.9638 (tpp) cc_final: 0.9016 (mtp) REVERT: D 524 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9251 (tpp) REVERT: D 713 MET cc_start: 0.8818 (mmm) cc_final: 0.8506 (tpp) REVERT: D 761 MET cc_start: 0.9318 (ttm) cc_final: 0.8968 (tpp) REVERT: D 852 MET cc_start: 0.9248 (mmm) cc_final: 0.8883 (mmm) REVERT: D 915 MET cc_start: 0.9512 (mmm) cc_final: 0.9196 (mmm) REVERT: D 934 MET cc_start: 0.9862 (mmm) cc_final: 0.9374 (mmm) outliers start: 22 outliers final: 12 residues processed: 109 average time/residue: 0.1927 time to fit residues: 34.8902 Evaluate side-chains 109 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 525 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 262 optimal weight: 0.5980 chunk 270 optimal weight: 8.9990 chunk 225 optimal weight: 20.0000 chunk 314 optimal weight: 0.0870 chunk 305 optimal weight: 8.9990 chunk 233 optimal weight: 0.1980 chunk 1 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 320 optimal weight: 8.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.029060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.022644 restraints weight = 457880.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.022644 restraints weight = 373855.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.022644 restraints weight = 373661.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.022644 restraints weight = 373661.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.022644 restraints weight = 373661.359| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28380 Z= 0.083 Angle : 0.509 11.342 38568 Z= 0.258 Chirality : 0.038 0.190 4416 Planarity : 0.003 0.031 4856 Dihedral : 3.506 21.268 3812 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.81 % Allowed : 5.87 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 3472 helix: 1.58 (0.13), residues: 1796 sheet: -0.44 (0.27), residues: 392 loop : -0.45 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 757 TYR 0.006 0.001 TYR D 914 PHE 0.015 0.001 PHE C 241 TRP 0.009 0.001 TRP C 514 HIS 0.001 0.000 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00175 (28380) covalent geometry : angle 0.50922 (38568) hydrogen bonds : bond 0.02594 ( 1164) hydrogen bonds : angle 3.80240 ( 3264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9379 (m-10) REVERT: A 431 MET cc_start: 0.9753 (mmm) cc_final: 0.9140 (mmm) REVERT: A 502 MET cc_start: 0.9586 (tpp) cc_final: 0.8826 (ttm) REVERT: A 524 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9166 (tpp) REVERT: A 713 MET cc_start: 0.8004 (tpp) cc_final: 0.7585 (tpp) REVERT: A 852 MET cc_start: 0.9312 (mmm) cc_final: 0.8777 (mmm) REVERT: A 915 MET cc_start: 0.9543 (mmm) cc_final: 0.9228 (mmm) REVERT: A 934 MET cc_start: 0.9848 (mmm) cc_final: 0.9375 (mmm) REVERT: A 1027 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7757 (m-10) REVERT: B 154 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9380 (m-10) REVERT: B 431 MET cc_start: 0.9747 (mmm) cc_final: 0.9129 (mmm) REVERT: B 502 MET cc_start: 0.9559 (tpp) cc_final: 0.8824 (ttm) REVERT: B 524 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9159 (tpp) REVERT: B 713 MET cc_start: 0.8367 (mmm) cc_final: 0.8029 (tpp) REVERT: B 852 MET cc_start: 0.9257 (mmm) cc_final: 0.8761 (mmm) REVERT: B 915 MET cc_start: 0.9552 (mmm) cc_final: 0.9240 (mmm) REVERT: B 934 MET cc_start: 0.9834 (mmm) cc_final: 0.9324 (mmm) REVERT: B 1027 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: C 154 PHE cc_start: 0.9801 (OUTLIER) cc_final: 0.9366 (m-10) REVERT: C 431 MET cc_start: 0.9752 (mmm) cc_final: 0.9137 (mmm) REVERT: C 502 MET cc_start: 0.9575 (tpp) cc_final: 0.8824 (ttm) REVERT: C 524 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9144 (tpp) REVERT: C 713 MET cc_start: 0.8425 (mmm) cc_final: 0.8092 (tpp) REVERT: C 761 MET cc_start: 0.9428 (ttm) cc_final: 0.9033 (tpp) REVERT: C 852 MET cc_start: 0.9216 (mmm) cc_final: 0.8723 (mmm) REVERT: C 915 MET cc_start: 0.9538 (mmm) cc_final: 0.9217 (mmm) REVERT: C 934 MET cc_start: 0.9841 (mmm) cc_final: 0.9354 (mmm) REVERT: C 1027 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: D 154 PHE cc_start: 0.9806 (OUTLIER) cc_final: 0.9388 (m-10) REVERT: D 431 MET cc_start: 0.9752 (mmm) cc_final: 0.9135 (mmm) REVERT: D 502 MET cc_start: 0.9562 (tpp) cc_final: 0.8809 (ttm) REVERT: D 524 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9153 (tpp) REVERT: D 713 MET cc_start: 0.8579 (mmm) cc_final: 0.8176 (tpp) REVERT: D 852 MET cc_start: 0.9242 (mmm) cc_final: 0.8769 (mmm) REVERT: D 915 MET cc_start: 0.9548 (mmm) cc_final: 0.9233 (mmm) REVERT: D 934 MET cc_start: 0.9845 (mmm) cc_final: 0.9354 (mmm) REVERT: D 1027 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7718 (m-10) outliers start: 24 outliers final: 3 residues processed: 112 average time/residue: 0.1952 time to fit residues: 36.3149 Evaluate side-chains 103 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 1027 PHE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 1027 PHE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 1027 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 280 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 211 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN B 161 ASN C 161 ASN D 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.029118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022562 restraints weight = 463958.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022562 restraints weight = 380563.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022562 restraints weight = 380563.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022562 restraints weight = 380563.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.022562 restraints weight = 380563.563| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28380 Z= 0.129 Angle : 0.553 10.263 38568 Z= 0.279 Chirality : 0.037 0.167 4416 Planarity : 0.003 0.029 4856 Dihedral : 3.578 22.772 3812 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.68 % Allowed : 6.75 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3472 helix: 1.60 (0.13), residues: 1800 sheet: -0.47 (0.27), residues: 400 loop : -0.36 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 382 TYR 0.008 0.001 TYR B1060 PHE 0.021 0.001 PHE D 492 TRP 0.009 0.001 TRP D 789 HIS 0.004 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00274 (28380) covalent geometry : angle 0.55272 (38568) hydrogen bonds : bond 0.02648 ( 1164) hydrogen bonds : angle 3.94439 ( 3264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9745 (mmm) cc_final: 0.9154 (mmm) REVERT: A 502 MET cc_start: 0.9597 (tpp) cc_final: 0.8818 (ttm) REVERT: A 713 MET cc_start: 0.8270 (tpp) cc_final: 0.7757 (tpp) REVERT: A 852 MET cc_start: 0.9152 (mmm) cc_final: 0.8834 (mmm) REVERT: A 915 MET cc_start: 0.9508 (mmm) cc_final: 0.9267 (mmm) REVERT: A 934 MET cc_start: 0.9857 (mmm) cc_final: 0.9393 (mmm) REVERT: A 969 MET cc_start: 0.6871 (tmm) cc_final: 0.6564 (ppp) REVERT: A 1027 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: B 431 MET cc_start: 0.9744 (mmm) cc_final: 0.9155 (mmm) REVERT: B 502 MET cc_start: 0.9584 (tpp) cc_final: 0.8826 (ttm) REVERT: B 713 MET cc_start: 0.8751 (mmm) cc_final: 0.8367 (tpp) REVERT: B 852 MET cc_start: 0.9193 (mmm) cc_final: 0.8831 (mmm) REVERT: B 915 MET cc_start: 0.9534 (mmm) cc_final: 0.9291 (mmm) REVERT: B 934 MET cc_start: 0.9848 (mmm) cc_final: 0.9355 (mmm) REVERT: B 1027 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7676 (m-10) REVERT: C 431 MET cc_start: 0.9750 (mmm) cc_final: 0.9162 (mmm) REVERT: C 502 MET cc_start: 0.9573 (tpp) cc_final: 0.8803 (ttm) REVERT: C 713 MET cc_start: 0.8629 (mmm) cc_final: 0.8301 (tpp) REVERT: C 761 MET cc_start: 0.9449 (ttm) cc_final: 0.9062 (tpp) REVERT: C 852 MET cc_start: 0.9192 (mmm) cc_final: 0.8834 (mmm) REVERT: C 915 MET cc_start: 0.9518 (mmm) cc_final: 0.9270 (mmm) REVERT: C 934 MET cc_start: 0.9853 (mmm) cc_final: 0.9365 (mmm) REVERT: C 969 MET cc_start: 0.6630 (tmm) cc_final: 0.6375 (ppp) REVERT: C 1027 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7791 (m-10) REVERT: D 431 MET cc_start: 0.9751 (mmm) cc_final: 0.9169 (mmm) REVERT: D 502 MET cc_start: 0.9607 (tpp) cc_final: 0.8816 (ttm) REVERT: D 713 MET cc_start: 0.8774 (mmm) cc_final: 0.8400 (tpp) REVERT: D 852 MET cc_start: 0.9155 (mmm) cc_final: 0.8840 (mmm) REVERT: D 915 MET cc_start: 0.9530 (mmm) cc_final: 0.9287 (mmm) REVERT: D 934 MET cc_start: 0.9855 (mmm) cc_final: 0.9382 (mmm) REVERT: D 1027 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7413 (m-10) outliers start: 20 outliers final: 8 residues processed: 104 average time/residue: 0.1685 time to fit residues: 30.7392 Evaluate side-chains 100 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 1027 PHE Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 1027 PHE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 1027 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 69 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 HIS A1046 ASN B1016 HIS B1046 ASN C1016 HIS C1046 ASN D1016 HIS D1046 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.029231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.022659 restraints weight = 462993.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.022659 restraints weight = 346046.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.022659 restraints weight = 346047.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.022659 restraints weight = 346047.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.022659 restraints weight = 346047.164| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28380 Z= 0.179 Angle : 0.622 9.860 38568 Z= 0.313 Chirality : 0.037 0.183 4416 Planarity : 0.003 0.029 4856 Dihedral : 3.778 23.418 3812 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.27 % Allowed : 7.39 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 3472 helix: 1.48 (0.13), residues: 1800 sheet: -0.44 (0.26), residues: 400 loop : -0.35 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 520 TYR 0.011 0.001 TYR C 389 PHE 0.022 0.001 PHE A 269 TRP 0.013 0.001 TRP B 235 HIS 0.005 0.001 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00369 (28380) covalent geometry : angle 0.62220 (38568) hydrogen bonds : bond 0.03003 ( 1164) hydrogen bonds : angle 4.29539 ( 3264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9780 (mmm) cc_final: 0.9181 (mmm) REVERT: A 502 MET cc_start: 0.9610 (tpp) cc_final: 0.8967 (mtp) REVERT: A 713 MET cc_start: 0.8325 (tpp) cc_final: 0.7721 (tpp) REVERT: A 852 MET cc_start: 0.9157 (mmm) cc_final: 0.8798 (mmm) REVERT: A 915 MET cc_start: 0.9461 (mmm) cc_final: 0.9091 (mmm) REVERT: A 934 MET cc_start: 0.9884 (mmm) cc_final: 0.9422 (mmm) REVERT: A 969 MET cc_start: 0.7103 (tmm) cc_final: 0.6826 (ppp) REVERT: B 431 MET cc_start: 0.9771 (mmm) cc_final: 0.9169 (mmm) REVERT: B 502 MET cc_start: 0.9610 (tpp) cc_final: 0.8966 (mtp) REVERT: B 852 MET cc_start: 0.9180 (mmm) cc_final: 0.8783 (mmm) REVERT: B 915 MET cc_start: 0.9463 (mmm) cc_final: 0.9095 (mmm) REVERT: B 934 MET cc_start: 0.9884 (mmm) cc_final: 0.9405 (mmm) REVERT: B 969 MET cc_start: 0.6795 (tmm) cc_final: 0.6514 (ppp) REVERT: C 431 MET cc_start: 0.9785 (mmm) cc_final: 0.9196 (mmm) REVERT: C 502 MET cc_start: 0.9602 (tpp) cc_final: 0.8955 (mtp) REVERT: C 713 MET cc_start: 0.8785 (mmm) cc_final: 0.8379 (tpp) REVERT: C 761 MET cc_start: 0.9385 (ttm) cc_final: 0.9076 (tpp) REVERT: C 852 MET cc_start: 0.9183 (mmm) cc_final: 0.8796 (mmm) REVERT: C 915 MET cc_start: 0.9452 (mmm) cc_final: 0.9075 (mmm) REVERT: C 934 MET cc_start: 0.9886 (mmm) cc_final: 0.9412 (mmm) REVERT: C 969 MET cc_start: 0.6937 (tmm) cc_final: 0.6646 (ppp) REVERT: D 431 MET cc_start: 0.9766 (mmm) cc_final: 0.9156 (mmm) REVERT: D 502 MET cc_start: 0.9626 (tpp) cc_final: 0.8980 (mtp) REVERT: D 852 MET cc_start: 0.9149 (mmm) cc_final: 0.8793 (mmm) REVERT: D 915 MET cc_start: 0.9452 (mmm) cc_final: 0.9093 (mmm) REVERT: D 934 MET cc_start: 0.9886 (mmm) cc_final: 0.9413 (mmm) REVERT: D 969 MET cc_start: 0.6874 (tmm) cc_final: 0.6602 (ppp) outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 0.1690 time to fit residues: 28.4555 Evaluate side-chains 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 854 PHE Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 854 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 42 optimal weight: 10.0000 chunk 195 optimal weight: 30.0000 chunk 349 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.029186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.022582 restraints weight = 464191.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.022582 restraints weight = 379821.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.022582 restraints weight = 379821.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.022582 restraints weight = 379821.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.022582 restraints weight = 379821.793| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28380 Z= 0.175 Angle : 0.627 10.794 38568 Z= 0.317 Chirality : 0.038 0.214 4416 Planarity : 0.003 0.029 4856 Dihedral : 3.857 20.420 3812 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.41 % Allowed : 7.26 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3472 helix: 1.46 (0.13), residues: 1800 sheet: -0.22 (0.27), residues: 376 loop : -0.36 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 614 TYR 0.012 0.001 TYR D 389 PHE 0.018 0.001 PHE A 492 TRP 0.009 0.001 TRP B 235 HIS 0.005 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00361 (28380) covalent geometry : angle 0.62749 (38568) hydrogen bonds : bond 0.02902 ( 1164) hydrogen bonds : angle 4.35799 ( 3264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6440.17 seconds wall clock time: 111 minutes 12.85 seconds (6672.85 seconds total)