Starting phenix.real_space_refine on Tue Jul 7 01:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fgi_31582/07_2026/7fgi_31582.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 60 5.49 5 Mg 12 5.21 5 S 336 5.16 5 C 26520 2.51 5 N 7248 2.21 5 O 8100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42288 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 437, 3415 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3482 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 103 Unusual residues: {' MG': 1, ' ZN': 1, 'GTA': 1} Classifications: {'DNA': 1, 'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1, None: 4} Not linked: pdbres=" ZN A1001 " pdbres="SAH A1002 " Not linked: pdbres="SAH A1002 " pdbres="GTA A1003 " Not linked: pdbres="GTA A1003 " pdbres=" U A1004 " Not linked: pdbres=" G A1005 " pdbres=" MG A1006 " Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 134 44.094 168.197 61.283 1.00 0.00 S ATOM 1071 SG CYS A 141 46.875 170.987 61.145 1.00 0.00 S Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 6.33, per 1000 atoms: 0.15 Number of scatterers: 42288 At special positions: 0 Unit cell: (204.85, 204.85, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 336 16.00 P 60 15.00 Mg 12 11.99 O 8100 8.00 N 7248 7.00 C 26520 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10032 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 36.8% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.509A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.790A pdb=" N MET B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.662A pdb=" N LEU B 346 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 404 removed outlier: 3.508A pdb=" N SER B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.828A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.508A pdb=" N SER C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 473 Processing helix chain 'D' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU D 346 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 404 removed outlier: 3.509A pdb=" N SER D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 396 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 removed outlier: 3.510A pdb=" N SER E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 396 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'F' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 removed outlier: 3.607A pdb=" N ARG F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU F 346 " --> pdb=" O THR F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 404 removed outlier: 3.509A pdb=" N SER F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 396 " --> pdb=" O SER F 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 removed outlier: 3.607A pdb=" N ARG G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.788A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.831A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 removed outlier: 3.508A pdb=" N SER G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 396 " --> pdb=" O SER G 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 473 Processing helix chain 'H' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 removed outlier: 3.790A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 103 removed outlier: 3.546A pdb=" N ARG H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.828A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU H 346 " --> pdb=" O THR H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 404 removed outlier: 3.508A pdb=" N SER H 392 " --> pdb=" O ALA H 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 473 Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.057A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.662A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 removed outlier: 3.508A pdb=" N SER I 392 " --> pdb=" O ALA I 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 396 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 473 Processing helix chain 'J' and resid 13 through 22 removed outlier: 4.055A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 343 through 348 removed outlier: 3.663A pdb=" N LEU J 346 " --> pdb=" O THR J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 363 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 404 removed outlier: 3.509A pdb=" N SER J 392 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS J 396 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP J 401 " --> pdb=" O GLU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 473 Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.057A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.606A pdb=" N ARG K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 103 removed outlier: 3.544A pdb=" N ARG K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.664A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 removed outlier: 3.509A pdb=" N SER K 392 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS K 396 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 473 Processing helix chain 'L' and resid 13 through 22 removed outlier: 4.056A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.605A pdb=" N ARG L 41 " --> pdb=" O ALA L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.789A pdb=" N MET L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 103 removed outlier: 3.545A pdb=" N ARG L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.664A pdb=" N LEU L 346 " --> pdb=" O THR L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 363 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 404 removed outlier: 3.508A pdb=" N SER L 392 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 396 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 147 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA A 148 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL A 176 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR A 150 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE A 178 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 177 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 6.951A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS B 134 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 80 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B 81 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP B 63 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN B 151 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 148 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL B 176 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR B 150 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE B 178 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 177 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 281 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 287 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.951A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 147 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA C 148 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL C 176 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR C 150 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N PHE C 178 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 177 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 251 removed outlier: 6.950A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE D 61 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL D 81 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP D 63 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 147 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN D 151 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA D 148 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL D 176 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR D 150 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N PHE D 178 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 177 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 281 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 287 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 246 through 251 removed outlier: 6.950A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 81 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP E 63 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL E 147 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA E 148 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL E 176 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR E 150 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE E 178 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 177 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 246 through 251 removed outlier: 6.950A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 8.295A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE F 61 " --> pdb=" O HIS F 79 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL F 81 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP F 63 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL F 147 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA F 148 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL F 176 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR F 150 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N PHE F 178 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 177 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL F 287 " --> pdb=" O VAL F 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 251 removed outlier: 6.952A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ALA F 191 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.295A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL G 147 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA G 148 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL G 176 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR G 150 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE G 178 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY G 177 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.950A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 133 through 134 removed outlier: 8.293A pdb=" N CYS H 134 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS H 80 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL H 81 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL H 147 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA H 148 " --> pdb=" O TYR H 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL H 176 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR H 150 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N PHE H 178 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY H 177 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER H 281 " --> pdb=" O TYR H 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL H 287 " --> pdb=" O VAL H 279 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 246 through 251 removed outlier: 6.951A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL I 81 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL I 147 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA I 148 " --> pdb=" O TYR I 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL I 176 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR I 150 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE I 178 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 177 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 246 through 251 removed outlier: 6.951A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 133 through 134 removed outlier: 8.295A pdb=" N CYS J 134 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS J 80 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL J 147 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN J 151 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA J 148 " --> pdb=" O TYR J 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL J 176 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR J 150 " --> pdb=" O VAL J 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE J 178 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY J 177 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 246 through 251 removed outlier: 6.951A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA J 191 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL K 147 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA K 148 " --> pdb=" O TYR K 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL K 176 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR K 150 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE K 178 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY K 177 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 246 through 251 removed outlier: 6.950A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 303 through 308 removed outlier: 4.049A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.293A pdb=" N CYS L 134 " --> pdb=" O TYR L 78 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS L 80 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE L 61 " --> pdb=" O HIS L 79 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL L 81 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP L 63 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 147 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA L 148 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL L 176 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR L 150 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N PHE L 178 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY L 177 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL L 287 " --> pdb=" O VAL L 279 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 246 through 251 removed outlier: 6.951A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA L 191 " --> pdb=" O TYR L 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 303 through 308 removed outlier: 4.048A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) 1800 hydrogen bonds defined for protein. 5112 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: 11.32 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13276 1.34 - 1.46: 7240 1.46 - 1.58: 22120 1.58 - 1.69: 120 1.69 - 1.81: 504 Bond restraints: 43260 Sorted by residual: bond pdb=" C3B GTA D1003 " pdb=" O3B GTA D1003 " ideal model delta sigma weight residual 1.404 1.623 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C3B GTA B1003 " pdb=" O3B GTA B1003 " ideal model delta sigma weight residual 1.404 1.622 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C3B GTA E1003 " pdb=" O3B GTA E1003 " ideal model delta sigma weight residual 1.404 1.622 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C3B GTA K1003 " pdb=" O3B GTA K1003 " ideal model delta sigma weight residual 1.404 1.622 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C3B GTA L1003 " pdb=" O3B GTA L1003 " ideal model delta sigma weight residual 1.404 1.622 -0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 43255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 57743 2.36 - 4.73: 826 4.73 - 7.09: 172 7.09 - 9.46: 95 9.46 - 11.82: 48 Bond angle restraints: 58884 Sorted by residual: angle pdb=" CG SAH G1002 " pdb=" SD SAH G1002 " pdb=" C5' SAH G1002 " ideal model delta sigma weight residual 101.77 89.95 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CG SAH I1002 " pdb=" SD SAH I1002 " pdb=" C5' SAH I1002 " ideal model delta sigma weight residual 101.77 89.96 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CG SAH J1002 " pdb=" SD SAH J1002 " pdb=" C5' SAH J1002 " ideal model delta sigma weight residual 101.77 89.98 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CG SAH A1002 " pdb=" SD SAH A1002 " pdb=" C5' SAH A1002 " ideal model delta sigma weight residual 101.77 90.01 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CG SAH F1002 " pdb=" SD SAH F1002 " pdb=" C5' SAH F1002 " ideal model delta sigma weight residual 101.77 90.01 11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 58879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 22417 17.73 - 35.47: 2637 35.47 - 53.20: 986 53.20 - 70.94: 192 70.94 - 88.67: 48 Dihedral angle restraints: 26280 sinusoidal: 10824 harmonic: 15456 Sorted by residual: dihedral pdb=" CA ALA K 191 " pdb=" C ALA K 191 " pdb=" N TYR K 192 " pdb=" CA TYR K 192 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ALA J 191 " pdb=" C ALA J 191 " pdb=" N TYR J 192 " pdb=" CA TYR J 192 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA D 191 " pdb=" C ALA D 191 " pdb=" N TYR D 192 " pdb=" CA TYR D 192 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 26277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4636 0.044 - 0.088: 1453 0.088 - 0.132: 534 0.132 - 0.176: 13 0.176 - 0.220: 24 Chirality restraints: 6660 Sorted by residual: chirality pdb=" C1A GTA I1003 " pdb=" C2A GTA I1003 " pdb=" N9 GTA I1003 " pdb=" O4A GTA I1003 " both_signs ideal model delta sigma weight residual False 2.37 2.59 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1A GTA E1003 " pdb=" C2A GTA E1003 " pdb=" N9 GTA E1003 " pdb=" O4A GTA E1003 " both_signs ideal model delta sigma weight residual False 2.37 2.58 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1A GTA F1003 " pdb=" C2A GTA F1003 " pdb=" N9 GTA F1003 " pdb=" O4A GTA F1003 " both_signs ideal model delta sigma weight residual False 2.37 2.58 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6657 not shown) Planarity restraints: 7296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 130 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO C 131 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 131 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 131 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 130 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO E 131 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 131 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 131 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 130 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO I 131 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 131 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 131 " 0.029 5.00e-02 4.00e+02 ... (remaining 7293 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 60 2.43 - 3.05: 24017 3.05 - 3.67: 56162 3.67 - 4.28: 90547 4.28 - 4.90: 153762 Nonbonded interactions: 324548 Sorted by model distance: nonbonded pdb=" O22 GTA G1003 " pdb="MG MG G1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA C1003 " pdb="MG MG C1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA F1003 " pdb="MG MG F1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA L1003 " pdb="MG MG L1006 " model vdw 1.814 2.170 nonbonded pdb=" O22 GTA K1003 " pdb="MG MG K1006 " model vdw 1.815 2.170 ... (remaining 324543 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.010 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: 0.050 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 45.120 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.009 0.276 43308 Z= 0.574 Angle : 0.845 11.823 58884 Z= 0.388 Chirality : 0.047 0.220 6660 Planarity : 0.005 0.052 7296 Dihedral : 17.939 88.673 16248 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.16 % Allowed : 14.82 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.11), residues: 5160 helix: 1.58 (0.14), residues: 1632 sheet: 1.27 (0.17), residues: 876 loop : -2.09 (0.09), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 467 TYR 0.014 0.001 TYR D 285 PHE 0.012 0.001 PHE I 241 TRP 0.008 0.001 TRP F 421 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.35 (43260) covalent geometry : angle 0.84513 / 0.39 (58884) hydrogen bonds : bond 0.19090 / 12.91 ( 1800) hydrogen bonds : angle 6.39199 / 4.45 ( 5112) metal coordination : bond 0.00249 / 0.16 ( 36) Misc. bond : bond 0.27531 / 18.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 256 time to evaluate : 1.464 Fit side-chains REVERT: B 123 MET cc_start: 0.6444 (mmp) cc_final: 0.5921 (mmp) REVERT: B 424 LYS cc_start: 0.6698 (mmpt) cc_final: 0.6262 (mmmt) REVERT: E 424 LYS cc_start: 0.6673 (mmpt) cc_final: 0.6262 (mmmt) REVERT: H 424 LYS cc_start: 0.6739 (mmpt) cc_final: 0.6336 (mmmt) REVERT: K 424 LYS cc_start: 0.6690 (mmpt) cc_final: 0.6270 (mmmt) outliers start: 96 outliers final: 48 residues processed: 328 average time/residue: 0.7226 time to fit residues: 291.0038 Evaluate side-chains 275 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 0.0970 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 ASN B 377 ASN E 377 ASN H 377 ASN J 377 ASN K 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073243 restraints weight = 228906.364| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.54 r_work: 0.2823 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43308 Z= 0.124 Angle : 0.566 11.519 58884 Z= 0.289 Chirality : 0.043 0.137 6660 Planarity : 0.005 0.047 7296 Dihedral : 9.405 72.814 6636 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.19 % Allowed : 16.71 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.11), residues: 5160 helix: 2.30 (0.14), residues: 1644 sheet: 0.75 (0.15), residues: 1092 loop : -1.96 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 20 TYR 0.010 0.001 TYR B 285 PHE 0.011 0.001 PHE J 264 TRP 0.007 0.001 TRP J 421 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (43260) covalent geometry : angle 0.56580 / 0.29 (58884) hydrogen bonds : bond 0.04768 / 3.18 ( 1800) hydrogen bonds : angle 4.57597 / 3.15 ( 5112) metal coordination : bond 0.00110 / 0.07 ( 36) Misc. bond : bond 0.00244 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 1.696 Fit side-chains REVERT: C 285 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: D 26 GLU cc_start: 0.6651 (mp0) cc_final: 0.6297 (pm20) REVERT: E 314 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8412 (tpp) REVERT: F 285 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: G 26 GLU cc_start: 0.6643 (mp0) cc_final: 0.6316 (pm20) REVERT: I 285 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: L 285 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7765 (m-80) outliers start: 53 outliers final: 16 residues processed: 283 average time/residue: 0.8231 time to fit residues: 281.3793 Evaluate side-chains 253 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 460 optimal weight: 10.0000 chunk 110 optimal weight: 0.0670 chunk 315 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 236 optimal weight: 0.0970 chunk 263 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 412 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 389 GLN F 389 GLN I 389 GLN L 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074676 restraints weight = 213929.277| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.14 r_work: 0.2863 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 43308 Z= 0.093 Angle : 0.496 13.202 58884 Z= 0.250 Chirality : 0.041 0.127 6660 Planarity : 0.004 0.043 7296 Dihedral : 8.341 78.675 6588 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.70 % Allowed : 16.89 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 5160 helix: 2.99 (0.14), residues: 1632 sheet: 0.97 (0.14), residues: 1164 loop : -1.85 (0.11), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.012 0.001 TYR A 382 PHE 0.011 0.001 PHE F 423 TRP 0.004 0.001 TRP D 421 HIS 0.002 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (43260) covalent geometry : angle 0.49627 / 0.25 (58884) hydrogen bonds : bond 0.03745 / 2.52 ( 1800) hydrogen bonds : angle 4.11311 / 2.84 ( 5112) metal coordination : bond 0.00107 / 0.07 ( 36) Misc. bond : bond 0.00097 / 0.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.814 Fit side-chains REVERT: A 26 GLU cc_start: 0.6619 (mp0) cc_final: 0.6331 (pm20) REVERT: B 424 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6595 (mmtt) REVERT: C 285 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: D 26 GLU cc_start: 0.6612 (mp0) cc_final: 0.6323 (pm20) REVERT: E 424 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6599 (mmtt) REVERT: F 26 GLU cc_start: 0.6896 (mp0) cc_final: 0.6551 (pm20) REVERT: F 285 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: G 26 GLU cc_start: 0.6655 (mp0) cc_final: 0.6368 (pm20) REVERT: H 424 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6604 (mmtt) REVERT: I 26 GLU cc_start: 0.6872 (mp0) cc_final: 0.6505 (pm20) REVERT: I 285 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: J 26 GLU cc_start: 0.6669 (mp0) cc_final: 0.6386 (pm20) REVERT: K 424 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6617 (mmtt) REVERT: L 26 GLU cc_start: 0.6853 (mp0) cc_final: 0.6490 (pm20) REVERT: L 285 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7841 (m-80) outliers start: 31 outliers final: 12 residues processed: 268 average time/residue: 0.8183 time to fit residues: 264.0717 Evaluate side-chains 260 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 303 optimal weight: 0.6980 chunk 509 optimal weight: 0.8980 chunk 352 optimal weight: 0.0010 chunk 470 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 494 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 227 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 HIS D 157 HIS F 157 HIS I 157 HIS L 157 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074368 restraints weight = 213592.562| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.12 r_work: 0.2853 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 43308 Z= 0.092 Angle : 0.489 13.383 58884 Z= 0.247 Chirality : 0.041 0.127 6660 Planarity : 0.004 0.041 7296 Dihedral : 7.997 77.591 6582 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.67 % Allowed : 16.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5160 helix: 3.04 (0.14), residues: 1656 sheet: 1.26 (0.16), residues: 960 loop : -1.74 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 325 TYR 0.008 0.001 TYR E 150 PHE 0.011 0.001 PHE C 423 TRP 0.005 0.001 TRP F 421 HIS 0.002 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (43260) covalent geometry : angle 0.48862 / 0.25 (58884) hydrogen bonds : bond 0.03462 / 2.31 ( 1800) hydrogen bonds : angle 3.96741 / 2.74 ( 5112) metal coordination : bond 0.00108 / 0.07 ( 36) Misc. bond : bond 0.00009 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 1.572 Fit side-chains REVERT: A 26 GLU cc_start: 0.6651 (mp0) cc_final: 0.6363 (pm20) REVERT: C 26 GLU cc_start: 0.6908 (mp0) cc_final: 0.6537 (pm20) REVERT: C 285 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: D 26 GLU cc_start: 0.6658 (mp0) cc_final: 0.6378 (pm20) REVERT: F 26 GLU cc_start: 0.6915 (mp0) cc_final: 0.6542 (pm20) REVERT: F 285 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: G 26 GLU cc_start: 0.6668 (mp0) cc_final: 0.6385 (pm20) REVERT: I 26 GLU cc_start: 0.6935 (mp0) cc_final: 0.6578 (pm20) REVERT: I 285 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: J 26 GLU cc_start: 0.6667 (mp0) cc_final: 0.6380 (pm20) REVERT: L 26 GLU cc_start: 0.6985 (mp0) cc_final: 0.6619 (pm20) REVERT: L 285 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7990 (m-80) outliers start: 30 outliers final: 14 residues processed: 275 average time/residue: 0.8308 time to fit residues: 275.9899 Evaluate side-chains 253 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 427 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 366 optimal weight: 0.1980 chunk 220 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.068905 restraints weight = 212058.358| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.13 r_work: 0.2733 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 43308 Z= 0.167 Angle : 0.585 12.787 58884 Z= 0.307 Chirality : 0.044 0.134 6660 Planarity : 0.005 0.041 7296 Dihedral : 8.481 80.254 6580 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.15 % Allowed : 17.27 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.12), residues: 5160 helix: 2.89 (0.14), residues: 1644 sheet: 1.26 (0.17), residues: 888 loop : -1.86 (0.10), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 289 TYR 0.012 0.001 TYR E 285 PHE 0.013 0.002 PHE B 183 TRP 0.008 0.001 TRP J 421 HIS 0.005 0.001 HIS H 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (43260) covalent geometry : angle 0.58508 / 0.31 (58884) hydrogen bonds : bond 0.06169 / 4.13 ( 1800) hydrogen bonds : angle 4.37383 / 3.01 ( 5112) metal coordination : bond 0.00251 / 0.16 ( 36) Misc. bond : bond 0.00005 / 0.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 1.238 Fit side-chains REVERT: C 285 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: C 314 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8958 (ttt) REVERT: E 389 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: F 285 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: F 314 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8944 (ttt) REVERT: F 424 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6902 (mmtt) REVERT: H 389 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8585 (tm-30) REVERT: I 285 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: I 314 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8954 (ttt) REVERT: L 285 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: L 314 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8967 (ttt) outliers start: 51 outliers final: 21 residues processed: 270 average time/residue: 0.8433 time to fit residues: 274.5697 Evaluate side-chains 263 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 402 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 113 optimal weight: 2.9990 chunk 434 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 488 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 515 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069076 restraints weight = 214384.778| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.14 r_work: 0.2744 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 43308 Z= 0.158 Angle : 0.578 13.161 58884 Z= 0.303 Chirality : 0.044 0.135 6660 Planarity : 0.005 0.042 7296 Dihedral : 8.499 85.336 6580 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.17 % Allowed : 17.41 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 5160 helix: 2.82 (0.14), residues: 1644 sheet: 0.90 (0.16), residues: 1020 loop : -1.88 (0.10), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.011 0.001 TYR B 150 PHE 0.014 0.001 PHE B 183 TRP 0.007 0.001 TRP J 421 HIS 0.004 0.001 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (43260) covalent geometry : angle 0.57820 / 0.30 (58884) hydrogen bonds : bond 0.05786 / 3.87 ( 1800) hydrogen bonds : angle 4.36526 / 3.00 ( 5112) metal coordination : bond 0.00258 / 0.17 ( 36) Misc. bond : bond 0.00007 / 0.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 1.711 Fit side-chains REVERT: B 389 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: B 424 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6487 (mmtt) REVERT: C 285 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: C 314 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8929 (ttt) REVERT: E 389 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: E 424 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6519 (mmtt) REVERT: F 285 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: F 314 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8934 (ttt) REVERT: F 424 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6866 (mmtt) REVERT: H 424 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6525 (mmtt) REVERT: I 285 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: J 314 MET cc_start: 0.9282 (ttt) cc_final: 0.9021 (ttt) REVERT: K 389 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: K 424 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6461 (mmtt) REVERT: L 285 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8409 (m-80) outliers start: 52 outliers final: 22 residues processed: 271 average time/residue: 0.8096 time to fit residues: 265.8727 Evaluate side-chains 274 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 402 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 184 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 122 optimal weight: 0.6980 chunk 507 optimal weight: 0.9980 chunk 314 optimal weight: 8.9990 chunk 363 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 492 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 377 ASN E 377 ASN F 377 ASN H 377 ASN I 377 ASN L 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073116 restraints weight = 215361.916| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.19 r_work: 0.2822 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 43308 Z= 0.094 Angle : 0.489 10.375 58884 Z= 0.251 Chirality : 0.041 0.124 6660 Planarity : 0.004 0.041 7296 Dihedral : 8.055 88.489 6580 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.76 % Allowed : 17.54 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 5160 helix: 3.24 (0.14), residues: 1620 sheet: 0.89 (0.14), residues: 1212 loop : -1.76 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.008 0.001 TYR K 150 PHE 0.011 0.001 PHE F 423 TRP 0.004 0.001 TRP I 258 HIS 0.002 0.001 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (43260) covalent geometry : angle 0.48949 / 0.25 (58884) hydrogen bonds : bond 0.03631 / 2.42 ( 1800) hydrogen bonds : angle 4.04450 / 2.79 ( 5112) metal coordination : bond 0.00115 / 0.07 ( 36) Misc. bond : bond 0.00003 / 0.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 285 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: F 285 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: H 424 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6450 (mmtt) REVERT: I 285 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: I 314 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8946 (ttt) REVERT: L 285 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: L 314 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8943 (ttt) outliers start: 34 outliers final: 14 residues processed: 292 average time/residue: 0.8237 time to fit residues: 291.8022 Evaluate side-chains 282 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 313 optimal weight: 0.0980 chunk 342 optimal weight: 4.9990 chunk 478 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 93 optimal weight: 0.0020 chunk 55 optimal weight: 0.9980 chunk 337 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 393 optimal weight: 9.9990 chunk 323 optimal weight: 0.6980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.073103 restraints weight = 195386.676| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.06 r_work: 0.2825 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 43308 Z= 0.096 Angle : 0.492 9.525 58884 Z= 0.252 Chirality : 0.041 0.125 6660 Planarity : 0.004 0.041 7296 Dihedral : 7.950 88.658 6578 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.65 % Allowed : 17.99 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 5160 helix: 3.21 (0.14), residues: 1644 sheet: 1.01 (0.15), residues: 1092 loop : -1.74 (0.11), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 76 TYR 0.008 0.001 TYR B 150 PHE 0.011 0.001 PHE I 423 TRP 0.003 0.001 TRP G 394 HIS 0.002 0.001 HIS K 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (43260) covalent geometry : angle 0.49242 / 0.25 (58884) hydrogen bonds : bond 0.03764 / 2.52 ( 1800) hydrogen bonds : angle 3.97363 / 2.74 ( 5112) metal coordination : bond 0.00096 / 0.06 ( 36) Misc. bond : bond 0.00007 / 0.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 285 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: E 424 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6445 (mmtt) REVERT: F 285 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: H 424 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6428 (mmtt) REVERT: I 285 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: I 314 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8963 (ttt) REVERT: K 424 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6436 (mmtt) REVERT: L 285 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8192 (m-80) outliers start: 29 outliers final: 14 residues processed: 288 average time/residue: 0.8162 time to fit residues: 285.4142 Evaluate side-chains 282 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 128 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 152 optimal weight: 0.0370 chunk 276 optimal weight: 3.9990 chunk 486 optimal weight: 4.9990 chunk 455 optimal weight: 0.0770 chunk 308 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 118 optimal weight: 0.0060 chunk 257 optimal weight: 5.9990 overall best weight: 1.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.071509 restraints weight = 191939.390| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.04 r_work: 0.2790 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43308 Z= 0.118 Angle : 0.526 10.694 58884 Z= 0.272 Chirality : 0.042 0.130 6660 Planarity : 0.004 0.041 7296 Dihedral : 8.091 89.136 6578 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.67 % Allowed : 18.08 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 5160 helix: 3.13 (0.14), residues: 1632 sheet: 0.98 (0.15), residues: 1092 loop : -1.76 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 289 TYR 0.009 0.001 TYR H 150 PHE 0.011 0.001 PHE B 183 TRP 0.005 0.001 TRP A 421 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (43260) covalent geometry : angle 0.52592 / 0.27 (58884) hydrogen bonds : bond 0.04647 / 3.10 ( 1800) hydrogen bonds : angle 4.08869 / 2.82 ( 5112) metal coordination : bond 0.00143 / 0.09 ( 36) Misc. bond : bond 0.00007 / 0.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6424 (mmtt) REVERT: C 285 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: E 424 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6441 (mmtt) REVERT: F 285 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: H 424 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6418 (mmtt) REVERT: I 285 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: I 314 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.8994 (ttt) REVERT: K 424 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6435 (mmtt) REVERT: L 285 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: L 314 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8980 (ttt) outliers start: 30 outliers final: 14 residues processed: 285 average time/residue: 0.8280 time to fit residues: 286.6986 Evaluate side-chains 286 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 22 optimal weight: 2.9990 chunk 416 optimal weight: 0.7980 chunk 495 optimal weight: 0.4980 chunk 290 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 295 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 496 optimal weight: 4.9990 chunk 367 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074553 restraints weight = 201026.980| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.11 r_work: 0.2854 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 43308 Z= 0.088 Angle : 0.477 10.247 58884 Z= 0.243 Chirality : 0.040 0.121 6660 Planarity : 0.004 0.040 7296 Dihedral : 7.776 89.573 6578 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.52 % Allowed : 18.28 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 5160 helix: 3.30 (0.14), residues: 1632 sheet: 0.98 (0.14), residues: 1284 loop : -1.73 (0.11), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 110 TYR 0.007 0.001 TYR L 150 PHE 0.010 0.001 PHE F 423 TRP 0.003 0.000 TRP L 258 HIS 0.002 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (43260) covalent geometry : angle 0.47736 / 0.24 (58884) hydrogen bonds : bond 0.03143 / 2.10 ( 1800) hydrogen bonds : angle 3.87652 / 2.68 ( 5112) metal coordination : bond 0.00088 / 0.06 ( 36) Misc. bond : bond 0.00004 / 0.00 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 2.052 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: C 285 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: D 424 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6936 (mmtt) REVERT: E 424 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6431 (mmtt) REVERT: F 285 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: H 424 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6428 (mmtt) REVERT: I 285 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: K 424 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6441 (mmtt) REVERT: L 285 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8044 (m-80) outliers start: 23 outliers final: 13 residues processed: 305 average time/residue: 0.7752 time to fit residues: 289.4089 Evaluate side-chains 295 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 424 LYS Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 424 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 293 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 355 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 chunk 339 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 480 optimal weight: 10.0000 chunk 449 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 504 optimal weight: 0.0030 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN C 377 ASN D 377 ASN E 377 ASN F 377 ASN G 377 ASN H 377 ASN I 377 ASN J 377 ASN K 377 ASN L 377 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.073153 restraints weight = 222974.323| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.28 r_work: 0.2812 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43308 Z= 0.094 Angle : 0.492 11.051 58884 Z= 0.250 Chirality : 0.041 0.125 6660 Planarity : 0.004 0.041 7296 Dihedral : 7.765 89.836 6577 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.49 % Allowed : 18.71 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 5160 helix: 3.23 (0.14), residues: 1656 sheet: 1.04 (0.15), residues: 1092 loop : -1.67 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 289 TYR 0.008 0.001 TYR K 150 PHE 0.010 0.001 PHE L 264 TRP 0.003 0.001 TRP B 199 HIS 0.002 0.001 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (43260) covalent geometry : angle 0.49225 / 0.25 (58884) hydrogen bonds : bond 0.03617 / 2.42 ( 1800) hydrogen bonds : angle 3.87393 / 2.68 ( 5112) metal coordination : bond 0.00094 / 0.06 ( 36) Misc. bond : bond 0.00007 / 0.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14259.26 seconds wall clock time: 243 minutes 52.92 seconds (14632.92 seconds total)