Starting phenix.real_space_refine on Tue Sep 15 16:29:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fgi_31582/09_2026/7fgi_31582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fgi_31582/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7fgi_31582/09_2026/7fgi_31582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fgi_31582/09_2026/7fgi_31582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fgi_31582/09_2026/7fgi_31582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fgi_31582/09_2026/7fgi_31582.map" model { file = "/net/cci-nas-00/data/ceres_data/7fgi_31582/09_2026/7fgi_31582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fgi_31582/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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, 'RNAv2': 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 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: 6.72, per 1000 atoms: 0.16 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: 3.94 Conformation dependent library (CDL) restraints added in 3.4 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: 1.27 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: 10.28 Time building geometry restraints manager: 5.26 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: 57635 2.36 - 4.73: 898 4.73 - 7.09: 172 7.09 - 9.46: 95 9.46 - 11.82: 48 Bond angle restraints: 58848 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 58843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 22333 17.73 - 35.47: 2673 35.47 - 53.20: 986 53.20 - 70.94: 216 70.94 - 88.67: 60 Dihedral angle restraints: 26268 sinusoidal: 10812 harmonic: 15456 Sorted by residual: dihedral pdb=" C4' U F1004 " pdb=" C3' U F1004 " pdb=" C2' U F1004 " pdb=" C1' U F1004 " ideal model delta sinusoidal sigma weight residual 36.34 -35.35 71.69 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" C4' U G1004 " pdb=" C3' U G1004 " pdb=" C2' U G1004 " pdb=" C1' U G1004 " ideal model delta sinusoidal sigma weight residual 36.34 -35.32 71.67 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" C4' U D1004 " pdb=" C3' U D1004 " pdb=" C2' U D1004 " pdb=" C1' U D1004 " ideal model delta sinusoidal sigma weight residual 36.35 -35.32 71.66 1 3.10e+00 1.04e-01 6.85e+02 ... (remaining 26265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5178 0.054 - 0.107: 1194 0.107 - 0.161: 222 0.161 - 0.215: 18 0.215 - 0.268: 48 Chirality restraints: 6660 Sorted by residual: chirality pdb=" C2' U K1004 " pdb=" C3' U K1004 " pdb=" O2' U K1004 " pdb=" C1' U K1004 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2' U F1004 " pdb=" C3' U F1004 " pdb=" O2' U F1004 " pdb=" C1' U F1004 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' U C1004 " pdb=" C3' U C1004 " pdb=" O2' U C1004 " pdb=" C1' U C1004 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.77e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 45.410 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.160 ------------------------------------------------------------------------------- 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 : 0.856 11.823 58848 Z= 0.390 Chirality : 0.050 0.268 6660 Planarity : 0.005 0.052 7296 Dihedral : 18.208 88.673 16236 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 0.00730 / 0.35 (43260) covalent geometry : angle 0.85615 / 0.39 (58848) 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 : 1.633 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: 0.7135 time to fit residues: 289.1214 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 : 1.686 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.099021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072959 restraints weight = 228124.498| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.45 r_work: 0.2821 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- 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 (8 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43308 Z= 0.131 Angle : 0.598 11.293 58848 Z= 0.297 Chirality : 0.045 0.212 6660 Planarity : 0.005 0.047 7296 Dihedral : 10.562 113.034 6624 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.19 % Allowed : 17.09 % Favored : 81.72 % 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: 0.09 (0.11), residues: 5160 helix: 2.28 (0.14), residues: 1632 sheet: 0.76 (0.15), residues: 1092 loop : -1.97 (0.10), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 20 TYR 0.009 0.001 TYR E 285 PHE 0.010 0.001 PHE I 264 TRP 0.006 0.001 TRP J 421 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (43260) covalent geometry : angle 0.59840 / 0.30 (58848) hydrogen bonds : bond 0.05166 / 3.45 ( 1800) hydrogen bonds : angle 4.65672 / 3.20 ( 5112) metal coordination : bond 0.00114 / 0.07 ( 36) Misc. bond : bond 0.00117 / 0.08 ( 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 297 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 1.633 Fit side-chains REVERT: A 26 GLU cc_start: 0.6671 (mp0) cc_final: 0.6324 (pm20) REVERT: B 123 MET cc_start: 0.8588 (mmp) cc_final: 0.8325 (mmp) REVERT: B 389 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: C 285 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: C 389 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: D 26 GLU cc_start: 0.6638 (mp0) cc_final: 0.6326 (pm20) REVERT: E 314 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8419 (tpp) REVERT: F 285 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: G 26 GLU cc_start: 0.6656 (mp0) cc_final: 0.6310 (pm20) REVERT: I 285 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: I 389 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: J 26 GLU cc_start: 0.6709 (mp0) cc_final: 0.6387 (pm20) REVERT: K 389 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: L 285 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: L 389 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7780 (tm-30) outliers start: 53 outliers final: 16 residues processed: 280 average time/residue: 0.7881 time to fit residues: 267.3865 Evaluate side-chains 260 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 389 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN 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 I residue 389 GLN 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 389 GLN Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 389 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 460 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 315 optimal weight: 0.7980 chunk 405 optimal weight: 2.9990 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: 0.0570 chunk 103 optimal weight: 0.6980 chunk 368 optimal weight: 3.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075260 restraints weight = 214361.357| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.28 r_work: 0.2862 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 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 = 0.2871 r_free = 0.2871 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: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43308 Z= 0.094 Angle : 0.501 13.107 58848 Z= 0.251 Chirality : 0.041 0.129 6660 Planarity : 0.004 0.043 7296 Dihedral : 10.092 141.718 6576 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.83 % Allowed : 16.98 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 5160 helix: 2.80 (0.14), residues: 1656 sheet: 1.05 (0.15), residues: 1044 loop : -1.86 (0.10), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 20 TYR 0.012 0.001 TYR A 382 PHE 0.011 0.001 PHE F 423 TRP 0.005 0.001 TRP D 421 HIS 0.002 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (43260) covalent geometry : angle 0.50137 / 0.25 (58848) hydrogen bonds : bond 0.03586 / 2.40 ( 1800) hydrogen bonds : angle 4.14593 / 2.86 ( 5112) metal coordination : bond 0.00103 / 0.07 ( 36) Misc. bond : bond 0.00082 / 0.06 ( 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 283 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 1.689 Fit side-chains REVERT: A 26 GLU cc_start: 0.6577 (mp0) cc_final: 0.6279 (pm20) REVERT: B 424 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6599 (mmtt) REVERT: C 26 GLU cc_start: 0.6885 (mp0) cc_final: 0.6515 (pm20) REVERT: C 285 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: D 26 GLU cc_start: 0.6588 (mp0) cc_final: 0.6295 (pm20) REVERT: E 424 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6601 (mmtt) REVERT: F 26 GLU cc_start: 0.6906 (mp0) cc_final: 0.6543 (pm20) REVERT: F 285 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: G 26 GLU cc_start: 0.6632 (mp0) cc_final: 0.6336 (pm20) REVERT: H 424 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6610 (mmtt) REVERT: I 285 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: J 26 GLU cc_start: 0.6640 (mp0) cc_final: 0.6343 (pm20) REVERT: K 424 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6557 (mmtt) REVERT: L 26 GLU cc_start: 0.6850 (mp0) cc_final: 0.6491 (pm20) REVERT: L 285 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.7760 (m-80) outliers start: 37 outliers final: 14 residues processed: 264 average time/residue: 0.8276 time to fit residues: 264.0896 Evaluate side-chains 257 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 509 optimal weight: 0.9980 chunk 352 optimal weight: 7.9990 chunk 470 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 494 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070084 restraints weight = 213462.682| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.26 r_work: 0.2762 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 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 = 0.2766 r_free = 0.2766 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: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43308 Z= 0.136 Angle : 0.565 13.347 58848 Z= 0.292 Chirality : 0.044 0.159 6660 Planarity : 0.005 0.042 7296 Dihedral : 10.108 138.539 6572 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.03 % Allowed : 17.36 % Favored : 81.60 % 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: 0.47 (0.12), residues: 5160 helix: 2.85 (0.14), residues: 1644 sheet: 1.31 (0.17), residues: 900 loop : -1.89 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 467 TYR 0.010 0.001 TYR E 150 PHE 0.012 0.001 PHE B 183 TRP 0.007 0.001 TRP A 421 HIS 0.004 0.001 HIS K 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (43260) covalent geometry : angle 0.56466 / 0.29 (58848) hydrogen bonds : bond 0.05611 / 3.75 ( 1800) hydrogen bonds : angle 4.38034 / 3.01 ( 5112) metal coordination : bond 0.00218 / 0.14 ( 36) Misc. bond : bond 0.00037 / 0.03 ( 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 290 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 1.557 Fit side-chains REVERT: B 389 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: C 285 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: C 314 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8961 (ttt) REVERT: F 285 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: F 314 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8944 (ttt) REVERT: H 424 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6410 (mmtt) REVERT: I 285 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: I 314 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8955 (ttt) REVERT: K 389 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: L 285 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: L 314 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8957 (ttt) outliers start: 46 outliers final: 15 residues processed: 273 average time/residue: 0.8163 time to fit residues: 268.6191 Evaluate side-chains 255 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 389 GLN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 314 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 F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 314 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 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 L residue 274 CYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET 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: 2.9990 chunk 321 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 497 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 366 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.094908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.068613 restraints weight = 211289.026| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.21 r_work: 0.2718 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43308 Z= 0.175 Angle : 0.608 13.158 58848 Z= 0.317 Chirality : 0.046 0.173 6660 Planarity : 0.005 0.042 7296 Dihedral : 10.378 142.575 6569 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.10 % Allowed : 17.70 % 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: 0.38 (0.12), residues: 5160 helix: 2.76 (0.14), residues: 1644 sheet: 1.18 (0.17), residues: 900 loop : -1.92 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 289 TYR 0.013 0.001 TYR B 285 PHE 0.015 0.002 PHE B 183 TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (43260) covalent geometry : angle 0.60837 / 0.32 (58848) hydrogen bonds : bond 0.06407 / 4.29 ( 1800) hydrogen bonds : angle 4.48364 / 3.08 ( 5112) metal coordination : bond 0.00308 / 0.20 ( 36) Misc. bond : bond 0.00069 / 0.05 ( 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 280 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.847 Fit side-chains REVERT: A 314 MET cc_start: 0.9284 (ttt) cc_final: 0.9036 (ttt) REVERT: B 389 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: B 424 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6451 (mmtt) REVERT: C 26 GLU cc_start: 0.7081 (mp0) cc_final: 0.6731 (pm20) REVERT: C 285 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: C 314 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.8947 (ttt) REVERT: D 314 MET cc_start: 0.9280 (ttt) cc_final: 0.9043 (ttt) REVERT: E 389 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: E 424 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6525 (mmtt) REVERT: F 285 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: F 314 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8932 (ttt) REVERT: H 389 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8533 (tm-30) REVERT: H 424 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6505 (mmtt) REVERT: H 441 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.9014 (mt0) REVERT: I 285 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: I 314 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8931 (ttt) REVERT: J 424 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6646 (mmpt) REVERT: K 389 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: K 424 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6428 (mmtt) REVERT: L 285 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: L 314 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8958 (ttt) outliers start: 49 outliers final: 19 residues processed: 266 average time/residue: 0.7923 time to fit residues: 255.2086 Evaluate side-chains 271 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 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 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 H residue 424 LYS Chi-restraints excluded: chain H residue 441 GLN 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 J residue 424 LYS 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 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: 1.9990 chunk 434 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 488 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 515 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 377 ASN F 377 ASN H 377 ASN I 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.068841 restraints weight = 211698.887| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.18 r_work: 0.2729 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43308 Z= 0.184 Angle : 0.620 13.534 58848 Z= 0.323 Chirality : 0.047 0.185 6660 Planarity : 0.005 0.045 7296 Dihedral : 10.381 140.809 6568 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.03 % Allowed : 18.01 % Favored : 80.95 % 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: 0.34 (0.12), residues: 5160 helix: 2.79 (0.14), residues: 1632 sheet: 0.94 (0.16), residues: 996 loop : -1.97 (0.10), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 289 TYR 0.013 0.002 TYR E 285 PHE 0.015 0.002 PHE E 183 TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS K 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (43260) covalent geometry : angle 0.62032 / 0.32 (58848) hydrogen bonds : bond 0.06475 / 4.34 ( 1800) hydrogen bonds : angle 4.51075 / 3.09 ( 5112) metal coordination : bond 0.00306 / 0.20 ( 36) Misc. bond : bond 0.00066 / 0.04 ( 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 300 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 1.694 Fit side-chains REVERT: B 389 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: B 441 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: C 285 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: C 314 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8950 (ttt) REVERT: D 424 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6668 (mmpt) REVERT: E 389 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: E 441 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: F 285 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: F 314 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.8916 (ttt) REVERT: F 424 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6856 (mmtt) REVERT: G 424 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6676 (mmpt) REVERT: H 389 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: H 441 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8999 (mt0) REVERT: I 285 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: I 314 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8915 (ttt) REVERT: J 424 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6675 (mmpt) REVERT: K 389 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: K 424 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6498 (mmtt) REVERT: K 441 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: L 285 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: L 314 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8917 (ttt) outliers start: 46 outliers final: 15 residues processed: 281 average time/residue: 0.8220 time to fit residues: 280.2860 Evaluate side-chains 282 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 441 GLN 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 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 389 GLN Chi-restraints excluded: chain E residue 441 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 285 TYR Chi-restraints excluded: chain G residue 424 LYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 441 GLN 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 285 TYR Chi-restraints excluded: chain J residue 424 LYS 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 K residue 441 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 184 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 507 optimal weight: 0.9990 chunk 314 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 492 optimal weight: 0.5980 chunk 263 optimal weight: 4.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 K 377 ASN L 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072813 restraints weight = 216046.547| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.22 r_work: 0.2814 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 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: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.3083 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= 0.097 Angle : 0.510 12.963 58848 Z= 0.259 Chirality : 0.042 0.127 6660 Planarity : 0.004 0.043 7296 Dihedral : 9.774 138.052 6564 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.63 % Allowed : 18.13 % 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: 0.74 (0.12), residues: 5160 helix: 3.17 (0.14), residues: 1620 sheet: 0.84 (0.14), residues: 1212 loop : -1.81 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 76 TYR 0.008 0.001 TYR B 150 PHE 0.011 0.001 PHE F 423 TRP 0.004 0.001 TRP B 258 HIS 0.002 0.001 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (43260) covalent geometry : angle 0.50971 / 0.26 (58848) hydrogen bonds : bond 0.03781 / 2.53 ( 1800) hydrogen bonds : angle 4.12030 / 2.83 ( 5112) metal coordination : bond 0.00107 / 0.07 ( 36) Misc. bond : bond 0.00044 / 0.03 ( 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 302 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 1.710 Fit side-chains REVERT: B 424 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6483 (mmtt) REVERT: C 285 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: E 424 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6506 (mmtt) REVERT: F 285 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: F 424 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6815 (mmtt) REVERT: H 424 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6462 (mmtt) REVERT: I 285 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: K 424 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6492 (mmtt) REVERT: L 285 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8161 (m-80) outliers start: 28 outliers final: 8 residues processed: 293 average time/residue: 0.8296 time to fit residues: 295.6671 Evaluate side-chains 281 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 285 TYR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 424 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 313 optimal weight: 0.0970 chunk 342 optimal weight: 3.9990 chunk 478 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 337 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 393 optimal weight: 0.1980 chunk 323 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.096586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.070836 restraints weight = 195874.596| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.13 r_work: 0.2776 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43308 Z= 0.131 Angle : 0.553 11.459 58848 Z= 0.286 Chirality : 0.043 0.148 6660 Planarity : 0.005 0.042 7296 Dihedral : 9.901 137.473 6564 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.72 % Allowed : 18.13 % Favored : 81.15 % 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: 0.62 (0.12), residues: 5160 helix: 3.02 (0.14), residues: 1632 sheet: 0.90 (0.15), residues: 1092 loop : -1.81 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 289 TYR 0.010 0.001 TYR H 150 PHE 0.012 0.001 PHE B 183 TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS K 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (43260) covalent geometry : angle 0.55324 / 0.29 (58848) hydrogen bonds : bond 0.05070 / 3.39 ( 1800) hydrogen bonds : angle 4.21129 / 2.89 ( 5112) metal coordination : bond 0.00178 / 0.11 ( 36) Misc. bond : bond 0.00053 / 0.04 ( 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 300 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 1.761 Fit side-chains REVERT: B 424 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6481 (mmtt) REVERT: C 285 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: E 424 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6492 (mmtt) REVERT: E 441 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8190 (mt0) REVERT: F 285 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: F 424 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6841 (mmtt) REVERT: H 424 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6470 (mmtt) REVERT: I 285 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: K 424 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6466 (mmtt) REVERT: L 285 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8371 (m-80) outliers start: 32 outliers final: 12 residues processed: 286 average time/residue: 0.8123 time to fit residues: 283.0996 Evaluate side-chains 275 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR 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 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 E residue 441 GLN Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 424 LYS 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 H residue 441 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 128 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 152 optimal weight: 0.0770 chunk 276 optimal weight: 2.9990 chunk 486 optimal weight: 0.0270 chunk 455 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 341 optimal weight: 0.9990 chunk 118 optimal weight: 0.0970 chunk 257 optimal weight: 7.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.098326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.072787 restraints weight = 193019.006| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.13 r_work: 0.2814 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 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 = 0.2820 r_free = 0.2820 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: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.3132 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= 0.098 Angle : 0.505 11.358 58848 Z= 0.258 Chirality : 0.042 0.132 6660 Planarity : 0.004 0.041 7296 Dihedral : 9.698 136.732 6564 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.56 % Allowed : 18.26 % Favored : 81.18 % 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: 3.24 (0.14), residues: 1608 sheet: 0.89 (0.14), residues: 1212 loop : -1.75 (0.11), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 110 TYR 0.009 0.001 TYR E 150 PHE 0.010 0.001 PHE L 264 TRP 0.003 0.001 TRP I 258 HIS 0.002 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (43260) covalent geometry : angle 0.50545 / 0.26 (58848) hydrogen bonds : bond 0.03911 / 2.61 ( 1800) hydrogen bonds : angle 4.04975 / 2.78 ( 5112) metal coordination : bond 0.00112 / 0.07 ( 36) Misc. bond : bond 0.00041 / 0.03 ( 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 304 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6451 (mmtt) REVERT: B 441 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: C 285 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: E 424 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6475 (mmtt) REVERT: F 285 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: F 424 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6790 (mmtt) REVERT: H 424 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6464 (mmtt) REVERT: I 285 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: K 424 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6475 (mmtt) REVERT: L 285 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8179 (m-80) outliers start: 25 outliers final: 12 residues processed: 298 average time/residue: 0.7917 time to fit residues: 289.6068 Evaluate side-chains 290 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 274 CYS 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 424 LYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS 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 Chi-restraints excluded: chain L residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 22 optimal weight: 4.9990 chunk 416 optimal weight: 10.0000 chunk 495 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 295 optimal weight: 2.9990 chunk 204 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 496 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.097673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.071907 restraints weight = 201746.544| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.20 r_work: 0.2799 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 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 = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 43308 Z= 0.108 Angle : 0.524 11.615 58848 Z= 0.268 Chirality : 0.042 0.138 6660 Planarity : 0.004 0.041 7296 Dihedral : 9.711 136.539 6564 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.70 % Allowed : 18.49 % Favored : 80.82 % 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: 0.74 (0.12), residues: 5160 helix: 3.14 (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 B 150 PHE 0.011 0.001 PHE L 423 TRP 0.004 0.001 TRP A 421 HIS 0.003 0.001 HIS E 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (43260) covalent geometry : angle 0.52358 / 0.27 (58848) hydrogen bonds : bond 0.04290 / 2.87 ( 1800) hydrogen bonds : angle 4.05506 / 2.78 ( 5112) metal coordination : bond 0.00119 / 0.08 ( 36) Misc. bond : bond 0.00044 / 0.03 ( 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 304 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 1.781 Fit side-chains REVERT: B 424 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6457 (mmtt) REVERT: B 441 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: C 285 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: D 424 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6852 (mmtt) REVERT: E 424 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6462 (mmtt) REVERT: F 285 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: F 424 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6807 (mmtt) REVERT: H 424 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6460 (mmtt) REVERT: I 285 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: K 424 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6458 (mmtt) REVERT: L 285 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8315 (m-80) outliers start: 31 outliers final: 14 residues processed: 296 average time/residue: 0.7931 time to fit residues: 287.5836 Evaluate side-chains 297 residues out of total 4500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 285 TYR 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 410 VAL 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 424 LYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 274 CYS 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 Chi-restraints excluded: chain L residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 293 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 355 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 480 optimal weight: 6.9990 chunk 449 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 504 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.097536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.071499 restraints weight = 224768.694| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.32 r_work: 0.2791 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 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 = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43308 Z= 0.111 Angle : 0.526 11.498 58848 Z= 0.270 Chirality : 0.042 0.141 6660 Planarity : 0.004 0.041 7296 Dihedral : 9.725 136.680 6564 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.72 % Allowed : 18.46 % Favored : 80.82 % 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: 3.08 (0.14), residues: 1644 sheet: 0.97 (0.15), residues: 1092 loop : -1.75 (0.11), residues: 2424 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 0.010 0.001 PHE I 264 TRP 0.004 0.001 TRP D 421 HIS 0.003 0.001 HIS K 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (43260) covalent geometry : angle 0.52648 / 0.27 (58848) hydrogen bonds : bond 0.04378 / 2.93 ( 1800) hydrogen bonds : angle 4.06802 / 2.79 ( 5112) metal coordination : bond 0.00121 / 0.08 ( 36) Misc. bond : bond 0.00042 / 0.03 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13786.03 seconds wall clock time: 235 minutes 42.37 seconds (14142.37 seconds total)