Starting phenix.real_space_refine on Mon May 26 10:12:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5tji_8414/05_2025/5tji_8414.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tji_8414/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5tji_8414/05_2025/5tji_8414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tji_8414/05_2025/5tji_8414.map" model { file = "/net/cci-nas-00/data/ceres_data/5tji_8414/05_2025/5tji_8414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tji_8414/05_2025/5tji_8414.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} 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: C, B, D Time building chain proxies: 16.85, per 1000 atoms: 0.61 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: 5.96 Conformation dependent library (CDL) restraints added in 3.3 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: 3.22 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: 9.34 Time building geometry restraints manager: 7.06 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 57.040 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP B 789 HIS 0.002 0.001 HIS B 453 PHE 0.014 0.001 PHE A 482 TYR 0.011 0.001 TYR D 914 ARG 0.003 0.000 ARG C 984 Details of bonding type rmsd hydrogen bonds : bond 0.30568 ( 1164) hydrogen bonds : angle 8.32033 ( 3264) covalent geometry : bond 0.00667 (28380) covalent geometry : angle 0.98484 (38568) *********************** 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 : 2.942 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: 0.8247 (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: 0.9581 (tpp) REVERT: A 934 MET cc_start: 0.9616 (mmm) cc_final: 0.9003 (mmm) REVERT: A 969 MET cc_start: 0.8851 (mmm) cc_final: 0.8555 (ttm) 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: 0.8246 (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: 0.9581 (tpp) REVERT: B 934 MET cc_start: 0.9618 (mmm) cc_final: 0.9004 (mmm) REVERT: B 969 MET cc_start: 0.8846 (mmm) cc_final: 0.8555 (ttm) 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: 0.8247 (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: 0.9581 (tpp) REVERT: C 934 MET cc_start: 0.9617 (mmm) cc_final: 0.9004 (mmm) REVERT: C 969 MET cc_start: 0.8849 (mmm) cc_final: 0.8554 (ttm) 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: 0.8247 (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: 0.9581 (tpp) REVERT: D 934 MET cc_start: 0.9617 (mmm) cc_final: 0.9004 (mmm) REVERT: D 969 MET cc_start: 0.8848 (mmm) cc_final: 0.8555 (ttm) outliers start: 12 outliers final: 0 residues processed: 120 average time/residue: 0.4096 time to fit residues: 78.2530 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 : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 205 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 451 GLN A 453 HIS A 454 ASN A 786 HIS A 989 GLN B 161 ASN B 451 GLN B 453 HIS B 454 ASN B 786 HIS B 989 GLN C 451 GLN C 453 HIS C 454 ASN C 786 HIS C 989 GLN D 451 GLN D 453 HIS D 454 ASN D 786 HIS D 989 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.030060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.024042 restraints weight = 454323.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.024042 restraints weight = 345801.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.024041 restraints weight = 345455.774| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28380 Z= 0.127 Angle : 0.540 8.310 38568 Z= 0.276 Chirality : 0.039 0.132 4416 Planarity : 0.004 0.036 4856 Dihedral : 4.242 17.944 3812 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.54 % Allowed : 3.46 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3472 helix: -0.04 (0.12), residues: 1804 sheet: -2.49 (0.21), residues: 452 loop : -1.53 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 514 HIS 0.003 0.001 HIS B 740 PHE 0.038 0.001 PHE C 241 TYR 0.011 0.001 TYR B1025 ARG 0.003 0.000 ARG A 984 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 1164) hydrogen bonds : angle 4.34175 ( 3264) covalent geometry : bond 0.00262 (28380) covalent geometry : angle 0.54003 (38568) *********************** 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 108 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 3.009 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: 0.9798 (mmm) cc_final: 0.9547 (mtm) REVERT: A 502 MET cc_start: 0.9181 (tpp) cc_final: 0.8505 (ttm) REVERT: A 524 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9104 (mmm) REVERT: A 761 MET cc_start: 0.9472 (ttm) cc_final: 0.9223 (tmm) REVERT: A 934 MET cc_start: 0.9650 (mmm) cc_final: 0.9169 (mmm) REVERT: B 496 MET cc_start: 0.9776 (mmm) cc_final: 0.9512 (mtm) REVERT: B 502 MET cc_start: 0.9150 (tpp) cc_final: 0.8533 (ttm) REVERT: B 511 MET cc_start: 0.8603 (ttm) cc_final: 0.8403 (ttm) REVERT: B 524 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9071 (mmm) REVERT: B 761 MET cc_start: 0.9570 (ttm) cc_final: 0.9244 (tmm) REVERT: B 934 MET cc_start: 0.9643 (mmm) cc_final: 0.9179 (mmm) REVERT: C 496 MET cc_start: 0.9783 (mmm) cc_final: 0.9530 (mtm) REVERT: C 502 MET cc_start: 0.9119 (tpp) cc_final: 0.8521 (ttm) REVERT: C 761 MET cc_start: 0.9514 (ttm) cc_final: 0.9226 (tmm) REVERT: C 934 MET cc_start: 0.9649 (mmm) cc_final: 0.9175 (mmm) REVERT: D 496 MET cc_start: 0.9794 (mmm) cc_final: 0.9541 (mtm) REVERT: D 502 MET cc_start: 0.9190 (tpp) cc_final: 0.8527 (ttm) REVERT: D 524 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9086 (mmm) REVERT: D 761 MET cc_start: 0.9481 (ttm) cc_final: 0.9227 (tmm) REVERT: D 934 MET cc_start: 0.9638 (mmm) cc_final: 0.9162 (mmm) outliers start: 16 outliers final: 0 residues processed: 100 average time/residue: 0.3988 time to fit residues: 66.0192 Evaluate side-chains 95 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain B 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 308 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.029600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.024719 restraints weight = 459383.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.024718 restraints weight = 284741.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.024718 restraints weight = 284176.129| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28380 Z= 0.108 Angle : 0.470 6.410 38568 Z= 0.241 Chirality : 0.037 0.188 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.756 15.856 3812 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.51 % Allowed : 4.14 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3472 helix: 0.71 (0.13), residues: 1808 sheet: -1.93 (0.22), residues: 444 loop : -1.14 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 514 HIS 0.003 0.001 HIS B 740 PHE 0.025 0.001 PHE C 241 TYR 0.021 0.001 TYR C 914 ARG 0.009 0.001 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 1164) hydrogen bonds : angle 3.96883 ( 3264) covalent geometry : bond 0.00219 (28380) covalent geometry : angle 0.47022 (38568) *********************** 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 107 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 2.959 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: A 431 MET cc_start: 0.9700 (mmm) cc_final: 0.9473 (mtt) REVERT: A 496 MET cc_start: 0.9804 (mmm) cc_final: 0.9584 (mtm) REVERT: A 502 MET cc_start: 0.9269 (tpp) cc_final: 0.8741 (ttm) REVERT: A 713 MET cc_start: 0.8437 (mmm) cc_final: 0.7894 (tpp) REVERT: A 761 MET cc_start: 0.9651 (ttm) cc_final: 0.9226 (tpp) REVERT: A 821 MET cc_start: 0.9569 (tpt) cc_final: 0.9034 (tpt) REVERT: A 852 MET cc_start: 0.9492 (mmm) cc_final: 0.8829 (mmp) REVERT: A 934 MET cc_start: 0.9705 (mmm) cc_final: 0.9055 (mmm) REVERT: B 431 MET cc_start: 0.9695 (mmm) cc_final: 0.9457 (mtt) REVERT: B 496 MET cc_start: 0.9790 (mmm) cc_final: 0.9572 (mtm) REVERT: B 502 MET cc_start: 0.9194 (tpp) cc_final: 0.8734 (ttm) REVERT: B 713 MET cc_start: 0.8383 (mmm) cc_final: 0.7882 (tpp) REVERT: B 761 MET cc_start: 0.9679 (ttm) cc_final: 0.9233 (tpp) REVERT: B 821 MET cc_start: 0.9588 (tpt) cc_final: 0.9059 (tpt) REVERT: B 852 MET cc_start: 0.9492 (mmm) cc_final: 0.8803 (mmp) REVERT: B 915 MET cc_start: 0.9627 (mmm) cc_final: 0.9410 (mmm) REVERT: B 934 MET cc_start: 0.9710 (mmm) cc_final: 0.9063 (mmm) REVERT: C 431 MET cc_start: 0.9694 (mmm) cc_final: 0.9455 (mtt) REVERT: C 496 MET cc_start: 0.9787 (mmm) cc_final: 0.9571 (mtm) REVERT: C 502 MET cc_start: 0.9260 (tpp) cc_final: 0.8761 (ttm) REVERT: C 713 MET cc_start: 0.8382 (mmm) cc_final: 0.7876 (tpp) REVERT: C 761 MET cc_start: 0.9660 (ttm) cc_final: 0.9221 (tpp) REVERT: C 821 MET cc_start: 0.9558 (tpt) cc_final: 0.9024 (tpt) REVERT: C 852 MET cc_start: 0.9495 (mmm) cc_final: 0.8817 (mmp) REVERT: C 934 MET cc_start: 0.9714 (mmm) cc_final: 0.9066 (mmm) REVERT: D 431 MET cc_start: 0.9699 (mmm) cc_final: 0.9472 (mtt) REVERT: D 496 MET cc_start: 0.9796 (mmm) cc_final: 0.9577 (mtm) REVERT: D 502 MET cc_start: 0.9262 (tpp) cc_final: 0.8753 (ttm) REVERT: D 713 MET cc_start: 0.8423 (mmm) cc_final: 0.7896 (tpp) REVERT: D 761 MET cc_start: 0.9678 (ttm) cc_final: 0.9247 (tpp) REVERT: D 821 MET cc_start: 0.9597 (tpt) cc_final: 0.9068 (tpt) REVERT: D 852 MET cc_start: 0.9483 (mmm) cc_final: 0.8807 (mmp) REVERT: D 934 MET cc_start: 0.9705 (mmm) cc_final: 0.9062 (mmm) outliers start: 15 outliers final: 0 residues processed: 104 average time/residue: 0.3792 time to fit residues: 65.9038 Evaluate side-chains 92 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 16 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 188 optimal weight: 40.0000 chunk 92 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 141 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 354 HIS ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 ASN D 354 HIS ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.029354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.023183 restraints weight = 462382.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.023322 restraints weight = 358274.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.023322 restraints weight = 294704.752| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28380 Z= 0.131 Angle : 0.501 6.595 38568 Z= 0.251 Chirality : 0.037 0.141 4416 Planarity : 0.003 0.028 4856 Dihedral : 3.670 14.518 3812 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.14 % Allowed : 4.99 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3472 helix: 1.05 (0.13), residues: 1824 sheet: -1.64 (0.23), residues: 448 loop : -0.81 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 192 HIS 0.004 0.001 HIS C1016 PHE 0.019 0.001 PHE B 241 TYR 0.010 0.001 TYR C 914 ARG 0.004 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 1164) hydrogen bonds : angle 3.90479 ( 3264) covalent geometry : bond 0.00269 (28380) covalent geometry : angle 0.50085 (38568) *********************** 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 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 3.131 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: 0.9760 (mmm) cc_final: 0.9223 (mmm) REVERT: A 496 MET cc_start: 0.9777 (mmm) cc_final: 0.9517 (mtm) REVERT: A 502 MET cc_start: 0.9557 (tpp) cc_final: 0.8975 (mtp) REVERT: A 519 MET cc_start: 0.8950 (ttp) cc_final: 0.8711 (ptm) REVERT: A 524 MET cc_start: 0.9709 (mmm) cc_final: 0.9089 (tpp) REVERT: A 713 MET cc_start: 0.8298 (mmm) cc_final: 0.7902 (tpp) REVERT: A 761 MET cc_start: 0.9423 (ttm) cc_final: 0.9186 (tpp) REVERT: A 852 MET cc_start: 0.9223 (mmm) cc_final: 0.8766 (mmm) REVERT: A 934 MET cc_start: 0.9790 (mmm) cc_final: 0.9151 (mmm) REVERT: B 431 MET cc_start: 0.9748 (mmm) cc_final: 0.9215 (mmm) REVERT: B 496 MET cc_start: 0.9761 (mmm) cc_final: 0.9509 (mtm) REVERT: B 502 MET cc_start: 0.9489 (tpp) cc_final: 0.8654 (ttm) REVERT: B 519 MET cc_start: 0.9633 (mmm) cc_final: 0.9360 (ttm) REVERT: B 524 MET cc_start: 0.9659 (mmm) cc_final: 0.9069 (tpp) REVERT: B 713 MET cc_start: 0.8346 (mmm) cc_final: 0.7951 (tpp) REVERT: B 761 MET cc_start: 0.9518 (ttm) cc_final: 0.9197 (tpp) REVERT: B 852 MET cc_start: 0.9258 (mmm) cc_final: 0.8762 (mmm) REVERT: B 934 MET cc_start: 0.9786 (mmm) cc_final: 0.9150 (mmm) REVERT: C 431 MET cc_start: 0.9754 (mmm) cc_final: 0.9218 (mmm) REVERT: C 496 MET cc_start: 0.9765 (mmm) cc_final: 0.9513 (mtm) REVERT: C 502 MET cc_start: 0.9545 (tpp) cc_final: 0.8950 (mtp) REVERT: C 519 MET cc_start: 0.9057 (ttp) cc_final: 0.8790 (ptm) REVERT: C 713 MET cc_start: 0.8188 (mmm) cc_final: 0.7885 (tpp) REVERT: C 761 MET cc_start: 0.9449 (ttm) cc_final: 0.9180 (tpp) REVERT: C 852 MET cc_start: 0.9200 (mmm) cc_final: 0.8748 (mmm) REVERT: C 934 MET cc_start: 0.9791 (mmm) cc_final: 0.9148 (mmm) REVERT: D 431 MET cc_start: 0.9755 (mmm) cc_final: 0.9219 (mmm) REVERT: D 496 MET cc_start: 0.9780 (mmm) cc_final: 0.9528 (mtm) REVERT: D 502 MET cc_start: 0.9547 (tpp) cc_final: 0.8959 (mtp) REVERT: D 519 MET cc_start: 0.8973 (ttp) cc_final: 0.8730 (ptm) REVERT: D 524 MET cc_start: 0.9702 (mmm) cc_final: 0.9071 (tpp) REVERT: D 713 MET cc_start: 0.8356 (mmm) cc_final: 0.7947 (tpp) REVERT: D 761 MET cc_start: 0.9493 (ttm) cc_final: 0.9200 (tpp) REVERT: D 852 MET cc_start: 0.9191 (mmm) cc_final: 0.8747 (mmm) REVERT: D 934 MET cc_start: 0.9789 (mmm) cc_final: 0.9152 (mmm) outliers start: 4 outliers final: 0 residues processed: 96 average time/residue: 0.3963 time to fit residues: 63.5239 Evaluate side-chains 92 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 269 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 265 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 186 optimal weight: 7.9990 chunk 321 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- 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** A1046 ASN ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 ASN ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 ASN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.029213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.022861 restraints weight = 457816.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.022861 restraints weight = 359187.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.022861 restraints weight = 359188.256| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28380 Z= 0.139 Angle : 0.500 10.607 38568 Z= 0.252 Chirality : 0.036 0.127 4416 Planarity : 0.003 0.036 4856 Dihedral : 3.668 15.000 3812 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.14 % Allowed : 5.56 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3472 helix: 1.29 (0.13), residues: 1828 sheet: -1.24 (0.25), residues: 448 loop : -0.59 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 789 HIS 0.004 0.001 HIS B1016 PHE 0.018 0.001 PHE B 854 TYR 0.027 0.001 TYR B 914 ARG 0.004 0.000 ARG D 970 Details of bonding type rmsd hydrogen bonds : bond 0.02479 ( 1164) hydrogen bonds : angle 3.84705 ( 3264) covalent geometry : bond 0.00284 (28380) covalent geometry : angle 0.50021 (38568) *********************** 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 96 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 3.007 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: 0.9796 (mmm) cc_final: 0.9299 (mmm) REVERT: A 496 MET cc_start: 0.9764 (mmm) cc_final: 0.9547 (mtm) REVERT: A 502 MET cc_start: 0.9609 (tpp) cc_final: 0.8810 (mtp) REVERT: A 519 MET cc_start: 0.9077 (ttp) cc_final: 0.8749 (ptm) REVERT: A 713 MET cc_start: 0.8451 (mmm) cc_final: 0.8100 (tpp) REVERT: A 761 MET cc_start: 0.9313 (ttm) cc_final: 0.8960 (tpp) REVERT: A 852 MET cc_start: 0.9189 (mmm) cc_final: 0.8709 (mmm) REVERT: A 915 MET cc_start: 0.9216 (mmm) cc_final: 0.8905 (mmm) REVERT: A 934 MET cc_start: 0.9838 (mmm) cc_final: 0.9271 (mmm) REVERT: B 431 MET cc_start: 0.9784 (mmm) cc_final: 0.9281 (mmm) REVERT: B 496 MET cc_start: 0.9726 (mmm) cc_final: 0.9493 (mtm) REVERT: B 502 MET cc_start: 0.9594 (tpp) cc_final: 0.8832 (mtp) REVERT: B 713 MET cc_start: 0.8528 (mmm) cc_final: 0.8111 (tpp) REVERT: B 761 MET cc_start: 0.9458 (ttm) cc_final: 0.8961 (tpp) REVERT: B 852 MET cc_start: 0.9266 (mmm) cc_final: 0.8747 (mmm) REVERT: B 934 MET cc_start: 0.9835 (mmm) cc_final: 0.9271 (mmm) REVERT: C 431 MET cc_start: 0.9793 (mmm) cc_final: 0.9291 (mmm) REVERT: C 496 MET cc_start: 0.9721 (mmm) cc_final: 0.9507 (mtm) REVERT: C 502 MET cc_start: 0.9587 (tpp) cc_final: 0.8836 (mtp) REVERT: C 519 MET cc_start: 0.9102 (ttp) cc_final: 0.8899 (ptm) REVERT: C 524 MET cc_start: 0.9603 (mmm) cc_final: 0.9347 (tpp) REVERT: C 713 MET cc_start: 0.8607 (mmm) cc_final: 0.8139 (tpp) REVERT: C 761 MET cc_start: 0.9415 (ttm) cc_final: 0.8969 (tpp) REVERT: C 852 MET cc_start: 0.9272 (mmm) cc_final: 0.8741 (mmm) REVERT: C 915 MET cc_start: 0.9246 (mmm) cc_final: 0.8937 (mmm) REVERT: C 934 MET cc_start: 0.9836 (mmm) cc_final: 0.9293 (mmm) REVERT: D 431 MET cc_start: 0.9793 (mmm) cc_final: 0.9279 (mmm) REVERT: D 496 MET cc_start: 0.9753 (mmm) cc_final: 0.9532 (mtm) REVERT: D 502 MET cc_start: 0.9595 (tpp) cc_final: 0.8807 (mtp) REVERT: D 519 MET cc_start: 0.9097 (ttp) cc_final: 0.8755 (ptm) REVERT: D 713 MET cc_start: 0.8556 (mmm) cc_final: 0.8168 (tpp) REVERT: D 761 MET cc_start: 0.9426 (ttm) cc_final: 0.8967 (tpp) REVERT: D 852 MET cc_start: 0.9213 (mmm) cc_final: 0.8730 (mmm) REVERT: D 915 MET cc_start: 0.9254 (mmm) cc_final: 0.8946 (mmm) REVERT: D 934 MET cc_start: 0.9834 (mmm) cc_final: 0.9277 (mmm) outliers start: 4 outliers final: 0 residues processed: 96 average time/residue: 0.4012 time to fit residues: 64.8040 Evaluate side-chains 92 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 138 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1046 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.029105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.022894 restraints weight = 458721.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.023138 restraints weight = 333121.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.023382 restraints weight = 262147.769| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 28380 Z= 0.081 Angle : 0.459 7.736 38568 Z= 0.229 Chirality : 0.037 0.137 4416 Planarity : 0.003 0.029 4856 Dihedral : 3.525 21.692 3812 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.34 % Allowed : 5.80 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3472 helix: 1.37 (0.13), residues: 1828 sheet: -0.98 (0.25), residues: 452 loop : -0.58 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 514 HIS 0.002 0.000 HIS D1016 PHE 0.016 0.001 PHE B 241 TYR 0.007 0.001 TYR A 914 ARG 0.002 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.02325 ( 1164) hydrogen bonds : angle 3.68773 ( 3264) covalent geometry : bond 0.00172 (28380) covalent geometry : angle 0.45855 (38568) *********************** 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 102 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 3.004 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: 0.9775 (mmm) cc_final: 0.9189 (mmm) REVERT: A 502 MET cc_start: 0.9592 (tpp) cc_final: 0.8596 (ttm) REVERT: A 713 MET cc_start: 0.8496 (mmm) cc_final: 0.8072 (tpp) REVERT: A 777 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9425 (tp) REVERT: A 852 MET cc_start: 0.9211 (mmm) cc_final: 0.8727 (mmm) REVERT: A 915 MET cc_start: 0.9354 (mmm) cc_final: 0.8953 (mmm) REVERT: A 934 MET cc_start: 0.9812 (mmm) cc_final: 0.9230 (mmm) REVERT: B 431 MET cc_start: 0.9773 (mmm) cc_final: 0.9198 (mmm) REVERT: B 496 MET cc_start: 0.9692 (mmm) cc_final: 0.9468 (mtm) REVERT: B 502 MET cc_start: 0.9598 (tpp) cc_final: 0.8984 (mtp) REVERT: B 713 MET cc_start: 0.8746 (mmm) cc_final: 0.8138 (tpp) REVERT: B 777 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9459 (tp) REVERT: B 852 MET cc_start: 0.9331 (mmm) cc_final: 0.8755 (mmm) REVERT: B 915 MET cc_start: 0.9304 (mmm) cc_final: 0.8878 (mmm) REVERT: B 934 MET cc_start: 0.9806 (mmm) cc_final: 0.9233 (mmm) REVERT: C 431 MET cc_start: 0.9774 (mmm) cc_final: 0.9187 (mmm) REVERT: C 496 MET cc_start: 0.9705 (mmm) cc_final: 0.9476 (mtm) REVERT: C 502 MET cc_start: 0.9578 (tpp) cc_final: 0.8608 (ttm) REVERT: C 524 MET cc_start: 0.9498 (mmm) cc_final: 0.9277 (tpp) REVERT: C 713 MET cc_start: 0.8615 (mmm) cc_final: 0.8133 (tpp) REVERT: C 777 ILE cc_start: 0.9721 (OUTLIER) cc_final: 0.9471 (tp) REVERT: C 852 MET cc_start: 0.9318 (mmm) cc_final: 0.8737 (mmm) REVERT: C 915 MET cc_start: 0.9378 (mmm) cc_final: 0.8948 (mmm) REVERT: C 934 MET cc_start: 0.9806 (mmm) cc_final: 0.9226 (mmm) REVERT: D 431 MET cc_start: 0.9774 (mmm) cc_final: 0.9187 (mmm) REVERT: D 502 MET cc_start: 0.9590 (tpp) cc_final: 0.8596 (ttm) REVERT: D 713 MET cc_start: 0.8661 (mmm) cc_final: 0.8102 (tpp) REVERT: D 777 ILE cc_start: 0.9711 (OUTLIER) cc_final: 0.9450 (tp) REVERT: D 852 MET cc_start: 0.9287 (mmm) cc_final: 0.8761 (mmm) REVERT: D 915 MET cc_start: 0.9376 (mmm) cc_final: 0.8975 (mmm) REVERT: D 934 MET cc_start: 0.9810 (mmm) cc_final: 0.9235 (mmm) outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 0.4061 time to fit residues: 65.1231 Evaluate side-chains 100 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 821 MET Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 821 MET Chi-restraints excluded: chain D residue 777 ILE Chi-restraints excluded: chain D residue 821 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 168 optimal weight: 30.0000 chunk 236 optimal weight: 0.0470 chunk 10 optimal weight: 50.0000 chunk 204 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 255 optimal weight: 0.0570 chunk 241 optimal weight: 0.1980 chunk 257 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 overall best weight: 2.6600 ------------------------------------------------------------------------------- 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** A1046 ASN B1046 ASN D1046 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.029106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.022841 restraints weight = 458987.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.022841 restraints weight = 321247.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.022841 restraints weight = 321248.264| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 28380 Z= 0.085 Angle : 0.473 9.018 38568 Z= 0.236 Chirality : 0.037 0.132 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.472 22.552 3812 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.47 % Allowed : 6.28 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3472 helix: 1.40 (0.13), residues: 1820 sheet: -0.79 (0.26), residues: 452 loop : -0.55 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 514 HIS 0.002 0.001 HIS C1016 PHE 0.019 0.001 PHE A 492 TYR 0.011 0.001 TYR C 505 ARG 0.004 0.000 ARG C 520 Details of bonding type rmsd hydrogen bonds : bond 0.02320 ( 1164) hydrogen bonds : angle 3.68171 ( 3264) covalent geometry : bond 0.00181 (28380) covalent geometry : angle 0.47297 (38568) *********************** 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 106 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.9759 (mmm) cc_final: 0.9209 (mmm) REVERT: A 502 MET cc_start: 0.9620 (tpp) cc_final: 0.8698 (ttm) REVERT: A 524 MET cc_start: 0.9611 (mmm) cc_final: 0.9029 (tpp) REVERT: A 713 MET cc_start: 0.8752 (mmm) cc_final: 0.8183 (tpp) REVERT: A 777 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9372 (tp) REVERT: A 852 MET cc_start: 0.9187 (mmm) cc_final: 0.8826 (mmm) REVERT: A 915 MET cc_start: 0.9444 (mmm) cc_final: 0.9232 (mmm) REVERT: A 934 MET cc_start: 0.9821 (mmm) cc_final: 0.9286 (mmm) REVERT: B 431 MET cc_start: 0.9745 (mmm) cc_final: 0.9194 (mmm) REVERT: B 496 MET cc_start: 0.9708 (mmm) cc_final: 0.9472 (mtm) REVERT: B 502 MET cc_start: 0.9571 (tpp) cc_final: 0.9004 (mtp) REVERT: B 713 MET cc_start: 0.8673 (mmm) cc_final: 0.8143 (tpp) REVERT: B 777 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9437 (tp) REVERT: B 852 MET cc_start: 0.9201 (mmm) cc_final: 0.8825 (mmm) REVERT: B 915 MET cc_start: 0.9464 (mmm) cc_final: 0.9091 (mmm) REVERT: B 934 MET cc_start: 0.9810 (mmm) cc_final: 0.9271 (mmm) REVERT: C 431 MET cc_start: 0.9746 (mmm) cc_final: 0.9193 (mmm) REVERT: C 496 MET cc_start: 0.9726 (mmm) cc_final: 0.9499 (mtm) REVERT: C 502 MET cc_start: 0.9552 (tpp) cc_final: 0.8724 (ttm) REVERT: C 713 MET cc_start: 0.8805 (mmm) cc_final: 0.8200 (tpp) REVERT: C 777 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9425 (tp) REVERT: C 852 MET cc_start: 0.9217 (mmm) cc_final: 0.8824 (mmm) REVERT: C 915 MET cc_start: 0.9480 (mmm) cc_final: 0.9236 (mmm) REVERT: C 934 MET cc_start: 0.9816 (mmm) cc_final: 0.9283 (mmm) REVERT: D 431 MET cc_start: 0.9754 (mmm) cc_final: 0.9200 (mmm) REVERT: D 502 MET cc_start: 0.9612 (tpp) cc_final: 0.8704 (ttm) REVERT: D 524 MET cc_start: 0.9603 (mmm) cc_final: 0.9015 (tpp) REVERT: D 713 MET cc_start: 0.8783 (mmm) cc_final: 0.8199 (tpp) REVERT: D 777 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9413 (tp) REVERT: D 852 MET cc_start: 0.9188 (mmm) cc_final: 0.8827 (mmm) REVERT: D 915 MET cc_start: 0.9447 (mmm) cc_final: 0.9236 (mmm) REVERT: D 934 MET cc_start: 0.9814 (mmm) cc_final: 0.9271 (mmm) outliers start: 14 outliers final: 0 residues processed: 100 average time/residue: 0.3773 time to fit residues: 62.7699 Evaluate side-chains 92 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain D residue 777 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 124 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 345 optimal weight: 30.0000 chunk 223 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 250 optimal weight: 0.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 HIS B 715 HIS C 161 ASN C 715 HIS C1046 ASN D 161 ASN D 715 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.029110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.022895 restraints weight = 459741.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.022895 restraints weight = 357850.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.022895 restraints weight = 357850.625| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28380 Z= 0.079 Angle : 0.494 10.563 38568 Z= 0.244 Chirality : 0.038 0.252 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.405 24.190 3812 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.44 % Allowed : 6.45 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3472 helix: 1.40 (0.13), residues: 1804 sheet: -0.64 (0.26), residues: 452 loop : -0.61 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 514 HIS 0.002 0.000 HIS B 383 PHE 0.015 0.001 PHE A 492 TYR 0.006 0.001 TYR C1025 ARG 0.005 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.02298 ( 1164) hydrogen bonds : angle 3.66636 ( 3264) covalent geometry : bond 0.00169 (28380) covalent geometry : angle 0.49360 (38568) *********************** 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 101 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 2.946 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 154 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9472 (m-10) REVERT: A 431 MET cc_start: 0.9771 (mmm) cc_final: 0.9214 (mmm) REVERT: A 496 MET cc_start: 0.9514 (mtm) cc_final: 0.9284 (mtm) REVERT: A 502 MET cc_start: 0.9613 (tpp) cc_final: 0.8986 (mtp) REVERT: A 524 MET cc_start: 0.9554 (mmm) cc_final: 0.9208 (tpp) REVERT: A 713 MET cc_start: 0.8547 (mmm) cc_final: 0.8327 (tpp) REVERT: A 777 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9404 (tp) REVERT: A 915 MET cc_start: 0.9502 (mmm) cc_final: 0.9235 (mmm) REVERT: A 934 MET cc_start: 0.9826 (mmm) cc_final: 0.9282 (mmm) REVERT: A 1027 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: B 154 PHE cc_start: 0.9805 (OUTLIER) cc_final: 0.9481 (m-10) REVERT: B 431 MET cc_start: 0.9759 (mmm) cc_final: 0.9215 (mmm) REVERT: B 496 MET cc_start: 0.9719 (mmm) cc_final: 0.9494 (mtm) REVERT: B 502 MET cc_start: 0.9554 (tpp) cc_final: 0.8938 (mtp) REVERT: B 524 MET cc_start: 0.9372 (mmm) cc_final: 0.9083 (tpp) REVERT: B 713 MET cc_start: 0.8461 (mmm) cc_final: 0.8250 (tpp) REVERT: B 777 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9446 (tp) REVERT: B 915 MET cc_start: 0.9479 (mmm) cc_final: 0.9116 (mmm) REVERT: B 934 MET cc_start: 0.9817 (mmm) cc_final: 0.9263 (mmm) REVERT: B 1027 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7918 (m-10) REVERT: C 154 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9468 (m-10) REVERT: C 431 MET cc_start: 0.9755 (mmm) cc_final: 0.9209 (mmm) REVERT: C 496 MET cc_start: 0.9723 (mmm) cc_final: 0.9506 (mtm) REVERT: C 502 MET cc_start: 0.9548 (tpp) cc_final: 0.9009 (mtp) REVERT: C 713 MET cc_start: 0.8502 (mmm) cc_final: 0.8269 (tpp) REVERT: C 777 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9455 (tp) REVERT: C 915 MET cc_start: 0.9543 (mmm) cc_final: 0.9280 (mmm) REVERT: C 934 MET cc_start: 0.9822 (mmm) cc_final: 0.9286 (mmm) REVERT: C 1027 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: D 154 PHE cc_start: 0.9808 (OUTLIER) cc_final: 0.9489 (m-10) REVERT: D 431 MET cc_start: 0.9770 (mmm) cc_final: 0.9213 (mmm) REVERT: D 496 MET cc_start: 0.9493 (mtm) cc_final: 0.9259 (mtm) REVERT: D 502 MET cc_start: 0.9601 (tpp) cc_final: 0.8978 (mtp) REVERT: D 524 MET cc_start: 0.9548 (mmm) cc_final: 0.9203 (tpp) REVERT: D 777 ILE cc_start: 0.9641 (OUTLIER) cc_final: 0.9425 (tp) REVERT: D 915 MET cc_start: 0.9495 (mmm) cc_final: 0.9233 (mmm) REVERT: D 934 MET cc_start: 0.9817 (mmm) cc_final: 0.9254 (mmm) REVERT: D 1027 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.7816 (m-10) outliers start: 13 outliers final: 0 residues processed: 101 average time/residue: 0.3444 time to fit residues: 60.8321 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 : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 1027 PHE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 1027 PHE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 777 ILE 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 6 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 323 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.029234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.022798 restraints weight = 460699.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.022798 restraints weight = 360987.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.022798 restraints weight = 360972.527| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28380 Z= 0.113 Angle : 0.534 10.024 38568 Z= 0.265 Chirality : 0.037 0.226 4416 Planarity : 0.003 0.030 4856 Dihedral : 3.451 25.259 3812 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.47 % Allowed : 6.55 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3472 helix: 1.52 (0.13), residues: 1808 sheet: -0.36 (0.26), residues: 440 loop : -0.54 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS B 740 PHE 0.023 0.001 PHE B 269 TYR 0.008 0.001 TYR C 505 ARG 0.001 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.02440 ( 1164) hydrogen bonds : angle 3.77429 ( 3264) covalent geometry : bond 0.00240 (28380) covalent geometry : angle 0.53387 (38568) *********************** 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 102 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 3.076 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: 0.9802 (OUTLIER) cc_final: 0.9425 (m-10) REVERT: A 431 MET cc_start: 0.9740 (mmm) cc_final: 0.9150 (mmm) REVERT: A 496 MET cc_start: 0.9481 (mtm) cc_final: 0.9219 (mtm) REVERT: A 502 MET cc_start: 0.9600 (tpp) cc_final: 0.8632 (ttm) REVERT: A 524 MET cc_start: 0.9524 (mmm) cc_final: 0.9178 (tpp) REVERT: A 713 MET cc_start: 0.8678 (mmm) cc_final: 0.8439 (tpp) REVERT: A 777 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9464 (tp) REVERT: A 915 MET cc_start: 0.9503 (mmm) cc_final: 0.9221 (mmm) REVERT: A 934 MET cc_start: 0.9853 (mmm) cc_final: 0.9320 (mmm) REVERT: A 1027 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7714 (m-10) REVERT: B 154 PHE cc_start: 0.9803 (OUTLIER) cc_final: 0.9426 (m-10) REVERT: B 431 MET cc_start: 0.9740 (mmm) cc_final: 0.9147 (mmm) REVERT: B 496 MET cc_start: 0.9794 (mmm) cc_final: 0.9573 (mtm) REVERT: B 502 MET cc_start: 0.9558 (tpp) cc_final: 0.8875 (mtp) REVERT: B 524 MET cc_start: 0.9326 (mmm) cc_final: 0.9041 (tpp) REVERT: B 713 MET cc_start: 0.8608 (mmm) cc_final: 0.8359 (tpp) REVERT: B 915 MET cc_start: 0.9501 (mmm) cc_final: 0.9155 (mmm) REVERT: B 934 MET cc_start: 0.9845 (mmm) cc_final: 0.9291 (mmm) REVERT: B 1027 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.7920 (m-10) REVERT: C 154 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9427 (m-10) REVERT: C 274 MET cc_start: 0.9741 (ppp) cc_final: 0.9375 (pmm) REVERT: C 298 MET cc_start: 0.9566 (mmp) cc_final: 0.9325 (mmm) REVERT: C 431 MET cc_start: 0.9735 (mmm) cc_final: 0.9151 (mmm) REVERT: C 496 MET cc_start: 0.9802 (mmm) cc_final: 0.9576 (mtm) REVERT: C 502 MET cc_start: 0.9545 (tpp) cc_final: 0.8935 (mtp) REVERT: C 713 MET cc_start: 0.8630 (mmm) cc_final: 0.8402 (tpp) REVERT: C 777 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9456 (tp) REVERT: C 915 MET cc_start: 0.9533 (mmm) cc_final: 0.9252 (mmm) REVERT: C 934 MET cc_start: 0.9847 (mmm) cc_final: 0.9315 (mmm) REVERT: C 1027 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: D 154 PHE cc_start: 0.9807 (OUTLIER) cc_final: 0.9443 (m-10) REVERT: D 274 MET cc_start: 0.9728 (ppp) cc_final: 0.9352 (pmm) REVERT: D 298 MET cc_start: 0.9561 (mmp) cc_final: 0.9316 (mmm) REVERT: D 431 MET cc_start: 0.9740 (mmm) cc_final: 0.9146 (mmm) REVERT: D 496 MET cc_start: 0.9484 (mtm) cc_final: 0.9229 (mtm) REVERT: D 502 MET cc_start: 0.9582 (tpp) cc_final: 0.8618 (ttm) REVERT: D 524 MET cc_start: 0.9514 (mmm) cc_final: 0.9159 (tpp) REVERT: D 915 MET cc_start: 0.9500 (mmm) cc_final: 0.9220 (mmm) REVERT: D 934 MET cc_start: 0.9852 (mmm) cc_final: 0.9304 (mmm) REVERT: D 1027 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7654 (m-10) outliers start: 14 outliers final: 0 residues processed: 102 average time/residue: 0.3542 time to fit residues: 63.0080 Evaluate side-chains 98 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 1027 PHE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 1027 PHE Chi-restraints excluded: chain D residue 154 PHE 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 216 optimal weight: 0.6980 chunk 335 optimal weight: 30.0000 chunk 267 optimal weight: 0.0030 chunk 102 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 0.0470 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 ASN D1046 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.029374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.023003 restraints weight = 453609.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.023001 restraints weight = 324239.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.023001 restraints weight = 323342.922| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28380 Z= 0.089 Angle : 0.555 18.013 38568 Z= 0.266 Chirality : 0.038 0.205 4416 Planarity : 0.003 0.031 4856 Dihedral : 3.423 25.922 3812 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.54 % Allowed : 6.72 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3472 helix: 1.54 (0.13), residues: 1796 sheet: -0.15 (0.28), residues: 400 loop : -0.52 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 235 HIS 0.002 0.000 HIS A 243 PHE 0.021 0.001 PHE C 269 TYR 0.008 0.001 TYR A 268 ARG 0.005 0.000 ARG D 757 Details of bonding type rmsd hydrogen bonds : bond 0.02411 ( 1164) hydrogen bonds : angle 3.69565 ( 3264) covalent geometry : bond 0.00187 (28380) covalent geometry : angle 0.55533 (38568) ********************** 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 104 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 2.922 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: 0.9445 (m-10) REVERT: A 271 MET cc_start: 0.9743 (mmm) cc_final: 0.9543 (mmm) REVERT: A 431 MET cc_start: 0.9693 (mmm) cc_final: 0.9081 (mmm) REVERT: A 496 MET cc_start: 0.9489 (mtm) cc_final: 0.9235 (mtm) REVERT: A 502 MET cc_start: 0.9580 (tpp) cc_final: 0.9012 (mtp) REVERT: A 524 MET cc_start: 0.9473 (mmm) cc_final: 0.9138 (tpp) REVERT: A 777 ILE cc_start: 0.9662 (OUTLIER) cc_final: 0.9434 (tp) REVERT: A 915 MET cc_start: 0.9546 (mmm) cc_final: 0.9237 (mmm) REVERT: A 934 MET cc_start: 0.9836 (mmm) cc_final: 0.9290 (mmm) REVERT: A 1027 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: B 154 PHE cc_start: 0.9809 (OUTLIER) cc_final: 0.9454 (m-10) REVERT: B 271 MET cc_start: 0.9748 (mmm) cc_final: 0.9547 (mmm) REVERT: B 431 MET cc_start: 0.9701 (mmm) cc_final: 0.9087 (mmm) REVERT: B 496 MET cc_start: 0.9801 (mmm) cc_final: 0.9577 (mtm) REVERT: B 502 MET cc_start: 0.9520 (tpp) cc_final: 0.8927 (mtp) REVERT: B 524 MET cc_start: 0.9191 (mmm) cc_final: 0.8957 (tpp) REVERT: B 713 MET cc_start: 0.8367 (mmm) cc_final: 0.8061 (tpp) REVERT: B 915 MET cc_start: 0.9481 (mmm) cc_final: 0.9115 (mmm) REVERT: B 934 MET cc_start: 0.9826 (mmm) cc_final: 0.9253 (mmm) REVERT: B 1027 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7983 (m-10) REVERT: C 154 PHE cc_start: 0.9805 (OUTLIER) cc_final: 0.9441 (m-10) REVERT: C 431 MET cc_start: 0.9691 (mmm) cc_final: 0.9084 (mmm) REVERT: C 496 MET cc_start: 0.9799 (mmm) cc_final: 0.9576 (mtm) REVERT: C 502 MET cc_start: 0.9545 (tpp) cc_final: 0.9020 (mtp) REVERT: C 713 MET cc_start: 0.8372 (mmm) cc_final: 0.8088 (tpp) REVERT: C 777 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9483 (tp) REVERT: C 915 MET cc_start: 0.9561 (mmm) cc_final: 0.9276 (mmm) REVERT: C 934 MET cc_start: 0.9833 (mmm) cc_final: 0.9286 (mmm) REVERT: C 1027 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7927 (m-10) REVERT: D 154 PHE cc_start: 0.9806 (OUTLIER) cc_final: 0.9449 (m-10) REVERT: D 431 MET cc_start: 0.9699 (mmm) cc_final: 0.9083 (mmm) REVERT: D 496 MET cc_start: 0.9493 (mtm) cc_final: 0.9243 (mtm) REVERT: D 502 MET cc_start: 0.9563 (tpp) cc_final: 0.8986 (mtp) REVERT: D 524 MET cc_start: 0.9455 (mmm) cc_final: 0.9127 (tpp) REVERT: D 713 MET cc_start: 0.8112 (tpp) cc_final: 0.7427 (tpp) REVERT: D 915 MET cc_start: 0.9544 (mmm) cc_final: 0.9234 (mmm) REVERT: D 934 MET cc_start: 0.9834 (mmm) cc_final: 0.9273 (mmm) REVERT: D 1027 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7633 (m-10) outliers start: 16 outliers final: 0 residues processed: 100 average time/residue: 0.4040 time to fit residues: 70.5838 Evaluate side-chains 98 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 1027 PHE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 1027 PHE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 1027 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7003 > 50: distance: 24 - 45: 13.668 distance: 30 - 53: 21.605 distance: 35 - 61: 16.564 distance: 42 - 45: 12.471 distance: 43 - 72: 20.453 distance: 45 - 46: 12.310 distance: 46 - 47: 23.724 distance: 46 - 49: 13.716 distance: 47 - 48: 40.432 distance: 47 - 53: 31.923 distance: 49 - 50: 14.770 distance: 50 - 51: 3.614 distance: 50 - 52: 8.444 distance: 53 - 54: 8.830 distance: 54 - 55: 18.004 distance: 54 - 57: 24.135 distance: 55 - 56: 23.353 distance: 55 - 61: 17.129 distance: 57 - 58: 30.395 distance: 58 - 59: 18.882 distance: 58 - 60: 9.873 distance: 61 - 62: 5.687 distance: 62 - 63: 17.229 distance: 62 - 65: 23.352 distance: 63 - 64: 20.896 distance: 63 - 72: 23.876 distance: 65 - 66: 20.422 distance: 66 - 67: 24.839 distance: 66 - 68: 7.213 distance: 67 - 69: 30.521 distance: 68 - 70: 17.130 distance: 69 - 71: 11.766 distance: 70 - 71: 23.944 distance: 72 - 73: 18.254 distance: 73 - 74: 20.040 distance: 73 - 76: 13.151 distance: 74 - 75: 16.424 distance: 74 - 79: 20.731 distance: 76 - 77: 31.436 distance: 76 - 78: 35.926 distance: 79 - 80: 14.248 distance: 80 - 81: 13.842 distance: 80 - 83: 14.129 distance: 81 - 82: 16.766 distance: 81 - 87: 19.951 distance: 83 - 84: 18.937 distance: 84 - 85: 18.653 distance: 85 - 86: 19.772 distance: 87 - 88: 21.094 distance: 88 - 89: 17.495 distance: 88 - 91: 19.339 distance: 89 - 90: 11.221 distance: 89 - 98: 13.067 distance: 91 - 92: 31.887 distance: 92 - 93: 33.759 distance: 93 - 94: 12.201 distance: 94 - 95: 3.437 distance: 95 - 96: 25.049 distance: 95 - 97: 7.193 distance: 98 - 99: 7.400 distance: 99 - 100: 16.039 distance: 99 - 102: 27.292 distance: 100 - 101: 10.794 distance: 100 - 104: 31.367 distance: 102 - 103: 18.738 distance: 104 - 105: 35.875 distance: 105 - 106: 18.516 distance: 105 - 108: 17.129 distance: 106 - 107: 18.255 distance: 106 - 116: 14.831 distance: 108 - 109: 23.881 distance: 109 - 110: 26.079 distance: 109 - 111: 6.679 distance: 110 - 112: 10.253 distance: 111 - 113: 13.038 distance: 112 - 114: 20.613 distance: 113 - 114: 19.332 distance: 114 - 115: 9.023 distance: 116 - 117: 35.367 distance: 117 - 118: 20.383 distance: 117 - 120: 41.038 distance: 118 - 119: 41.384 distance: 118 - 125: 19.225 distance: 120 - 121: 30.975 distance: 121 - 122: 18.881 distance: 122 - 123: 13.061 distance: 123 - 124: 16.217 distance: 125 - 126: 10.571 distance: 125 - 131: 6.202 distance: 126 - 127: 13.311 distance: 127 - 128: 39.366 distance: 127 - 132: 34.324 distance: 129 - 130: 25.158 distance: 130 - 131: 34.181