Starting phenix.real_space_refine on Tue Aug 26 15:23:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qg2_4545/08_2025/6qg2_4545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qg2_4545/08_2025/6qg2_4545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qg2_4545/08_2025/6qg2_4545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qg2_4545/08_2025/6qg2_4545.map" model { file = "/net/cci-nas-00/data/ceres_data/6qg2_4545/08_2025/6qg2_4545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qg2_4545/08_2025/6qg2_4545.cif" } resolution = 4.55 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= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 177 5.16 5 C 24589 2.51 5 N 6619 2.21 5 O 7277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38664 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2967 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 20, 'TRANS': 354} Chain breaks: 8 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1967 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1967 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1036 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 108 residue: pdb=" N GLN F 414 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 414 " occ=0.00 residue: pdb=" N THR F 415 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR F 415 " occ=0.00 residue: pdb=" N MET F 416 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET F 416 " occ=0.00 residue: pdb=" N PHE F 417 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE F 417 " occ=0.00 residue: pdb=" N THR F 418 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR F 418 " occ=0.00 residue: pdb=" N LYS F 419 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS F 419 " occ=0.00 residue: pdb=" N ASN F 420 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN F 420 " occ=0.00 residue: pdb=" N ILE F 421 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE F 421 " occ=0.00 residue: pdb=" N GLN F 422 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 422 " occ=0.00 residue: pdb=" N ILE F 423 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE F 423 " occ=0.00 residue: pdb=" N GLN F 424 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 424 " occ=0.00 residue: pdb=" N ALA F 426 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA F 426 " occ=0.00 ... (remaining 96 not shown) Time building chain proxies: 8.74, per 1000 atoms: 0.23 Number of scatterers: 38664 At special positions: 0 Unit cell: (276.04, 164.82, 135.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 177 16.00 P 2 15.00 O 7277 8.00 N 6619 7.00 C 24589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9398 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 48 sheets defined 32.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.853A pdb=" N THR A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.656A pdb=" N ALA A 26 " --> pdb=" O MET A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 64 through 81 removed outlier: 4.475A pdb=" N ALA A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 4.047A pdb=" N CYS A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.201A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.771A pdb=" N ILE B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 4.386A pdb=" N ASN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.777A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 86 through 97 removed outlier: 4.291A pdb=" N CYS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 91 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.530A pdb=" N VAL B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 161 through 173 removed outlier: 3.764A pdb=" N LYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.921A pdb=" N ALA B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 82 through 108 removed outlier: 3.633A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.786A pdb=" N LEU C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 removed outlier: 3.644A pdb=" N THR C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LYS C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN C 225 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.693A pdb=" N MET C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 289 Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.767A pdb=" N ILE C 321 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 369 removed outlier: 4.078A pdb=" N ILE C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 36 through 55 removed outlier: 3.582A pdb=" N ALA D 54 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 78 removed outlier: 4.065A pdb=" N LEU D 63 " --> pdb=" O HIS D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 108 removed outlier: 3.730A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 Processing helix chain 'D' and resid 168 through 173 removed outlier: 3.719A pdb=" N GLN D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.569A pdb=" N ASP D 178 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 179 " --> pdb=" O ALA D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 179' Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.907A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 4.221A pdb=" N ASN D 225 " --> pdb=" O ASN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 289 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.814A pdb=" N VAL D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.752A pdb=" N LYS D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 330 " --> pdb=" O PRO D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 330' Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 360 through 367 removed outlier: 3.916A pdb=" N ILE D 364 " --> pdb=" O PHE D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 87 removed outlier: 3.830A pdb=" N TYR E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 180 through 190 removed outlier: 3.910A pdb=" N VAL E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.784A pdb=" N LEU E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 286 through 291' Processing helix chain 'E' and resid 403 through 412 removed outlier: 4.274A pdb=" N LYS E 412 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'F' and resid 257 through 262 removed outlier: 4.241A pdb=" N ASN F 262 " --> pdb=" O HIS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 405 through 412 Processing helix chain 'G' and resid 271 through 283 removed outlier: 4.473A pdb=" N LEU G 275 " --> pdb=" O HIS G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 307 removed outlier: 4.896A pdb=" N CYS G 293 " --> pdb=" O SER G 289 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 334 Processing helix chain 'G' and resid 337 through 354 Processing helix chain 'G' and resid 362 through 379 removed outlier: 3.546A pdb=" N ASP G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 393 Processing helix chain 'G' and resid 406 through 418 Processing helix chain 'G' and resid 436 through 446 Processing helix chain 'G' and resid 459 through 463 removed outlier: 3.739A pdb=" N PHE G 463 " --> pdb=" O ASP G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 499 Processing helix chain 'G' and resid 528 through 532 Processing helix chain 'G' and resid 582 through 586 removed outlier: 3.503A pdb=" N GLU G 585 " --> pdb=" O SER G 582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 586 " --> pdb=" O GLU G 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 582 through 586' Processing helix chain 'H' and resid 271 through 283 removed outlier: 3.861A pdb=" N LEU H 275 " --> pdb=" O HIS H 271 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 307 removed outlier: 3.599A pdb=" N CYS H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 334 Processing helix chain 'H' and resid 337 through 354 Processing helix chain 'H' and resid 359 through 379 removed outlier: 3.637A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 394 Processing helix chain 'H' and resid 406 through 419 Processing helix chain 'H' and resid 435 through 448 Processing helix chain 'H' and resid 459 through 464 removed outlier: 3.988A pdb=" N PHE H 463 " --> pdb=" O LEU H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 499 Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.893A pdb=" N LEU I 52 " --> pdb=" O ARG I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 71 removed outlier: 4.461A pdb=" N TYR I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 3.966A pdb=" N ILE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 126 Processing helix chain 'I' and resid 144 through 159 removed outlier: 4.448A pdb=" N MET I 148 " --> pdb=" O ASP I 144 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP I 159 " --> pdb=" O MET I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 216 No H-bonds generated for 'chain 'I' and resid 214 through 216' Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.037A pdb=" N VAL I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP I 222 " --> pdb=" O LEU I 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 217 through 222' Processing helix chain 'I' and resid 240 through 249 removed outlier: 4.298A pdb=" N LEU I 244 " --> pdb=" O SER I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 266 Processing helix chain 'I' and resid 288 through 300 Processing helix chain 'J' and resid 59 through 71 removed outlier: 3.867A pdb=" N THR J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.777A pdb=" N ILE J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 126 Processing helix chain 'J' and resid 145 through 159 Processing helix chain 'J' and resid 241 through 249 Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 287 through 300 Processing helix chain 'K' and resid 94 through 112 Processing helix chain 'K' and resid 113 through 120 removed outlier: 3.598A pdb=" N PHE K 119 " --> pdb=" O CYS K 115 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 removed outlier: 3.736A pdb=" N LEU K 126 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 138 removed outlier: 4.307A pdb=" N LYS K 137 " --> pdb=" O PRO K 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 138 " --> pdb=" O LEU K 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 133 through 138' Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.868A pdb=" N ALA K 144 " --> pdb=" O HIS K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 174 removed outlier: 3.530A pdb=" N LEU K 166 " --> pdb=" O SER K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 207 Processing helix chain 'K' and resid 240 through 256 removed outlier: 3.539A pdb=" N LEU K 244 " --> pdb=" O GLY K 240 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 120 removed outlier: 4.206A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 135 removed outlier: 4.026A pdb=" N LEU L 126 " --> pdb=" O PRO L 122 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TRP L 132 " --> pdb=" O LYS L 128 " (cutoff:3.500A) Proline residue: L 133 - end of helix Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 154 through 158 removed outlier: 3.668A pdb=" N GLY L 157 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'L' and resid 197 through 207 Processing helix chain 'L' and resid 240 through 257 removed outlier: 3.735A pdb=" N LEU L 244 " --> pdb=" O GLY L 240 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 201 through 211 removed outlier: 3.667A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 239 removed outlier: 3.827A pdb=" N SER M 230 " --> pdb=" O GLN M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 270 Processing helix chain 'M' and resid 290 through 302 removed outlier: 4.085A pdb=" N VAL M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE M 302 " --> pdb=" O ILE M 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 141 Processing helix chain 'N' and resid 113 through 121 Processing helix chain 'N' and resid 201 through 211 removed outlier: 3.557A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 239 removed outlier: 3.874A pdb=" N SER N 230 " --> pdb=" O GLN N 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 270 removed outlier: 4.326A pdb=" N LEU N 260 " --> pdb=" O GLU N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 302 removed outlier: 4.318A pdb=" N ILE N 302 " --> pdb=" O ILE N 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 141 Processing helix chain 'P' and resid 176 through 184 Processing helix chain 'P' and resid 187 through 199 removed outlier: 3.811A pdb=" N LEU P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 179 removed outlier: 4.245A pdb=" N THR A 177 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 153 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU A 127 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE A 227 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE A 284 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 229 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.764A pdb=" N ILE A 207 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.942A pdb=" N ARG B 150 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 128 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR B 154 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 125 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE B 195 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 127 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 197 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS B 129 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 194 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL B 230 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 196 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 227 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE B 284 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 229 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.512A pdb=" N LYS C 257 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 259 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 272 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 271 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 341 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.512A pdb=" N LYS C 257 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 259 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 258 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL C 295 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 260 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE C 348 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 350 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 331 through 333 removed outlier: 6.291A pdb=" N VAL G 451 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 426 " --> pdb=" O MET G 452 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA G 454 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL G 428 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 292 through 294 removed outlier: 6.101A pdb=" N VAL D 258 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 185 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE D 259 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 187 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLU D 184 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU D 214 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 186 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR D 216 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU D 241 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 213 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL D 243 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL D 215 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU H 557 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 264 through 265 Processing sheet with id=AA9, first strand: chain 'D' and resid 314 through 315 removed outlier: 3.618A pdb=" N GLU D 314 " --> pdb=" O THR D 338 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 338 " --> pdb=" O GLU D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 332 through 333 removed outlier: 7.511A pdb=" N THR H 398 " --> pdb=" O LYS H 425 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE H 427 " --> pdb=" O THR H 398 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE H 400 " --> pdb=" O ILE H 427 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL H 429 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR H 402 " --> pdb=" O VAL H 429 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR H 399 " --> pdb=" O TYR H 469 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 8.347A pdb=" N SER E 93 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA E 5 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL E 95 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 7 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN E 4 " --> pdb=" O ASP E 166 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 168 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 274 removed outlier: 3.638A pdb=" N PHE E 392 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.821A pdb=" N PHE E 223 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 134 through 136 removed outlier: 3.668A pdb=" N HIS F 134 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 278 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR F 390 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR F 198 " --> pdb=" O THR F 390 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 239 through 240 removed outlier: 3.757A pdb=" N TYR F 226 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE F 223 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I 224 " --> pdb=" O VAL F 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 444 through 447 removed outlier: 6.476A pdb=" N ASN F 445 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 464 " --> pdb=" O LEU F 480 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU F 497 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 466 through 467 removed outlier: 3.874A pdb=" N LEU F 467 " --> pdb=" O CYS F 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.549A pdb=" N LYS F 490 " --> pdb=" O TYR F 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 471 through 473 removed outlier: 3.779A pdb=" N CYS G 506 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 574 " --> pdb=" O GLY G 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY G 581 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 576 " --> pdb=" O LYS G 579 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 476 through 477 removed outlier: 3.664A pdb=" N SER G 476 " --> pdb=" O TYR G 484 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 483 " --> pdb=" O ALA G 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 476 through 477 Processing sheet with id=AC4, first strand: chain 'H' and resid 503 through 506 removed outlier: 7.206A pdb=" N VAL H 503 " --> pdb=" O PRO H 571 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY H 573 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS H 575 " --> pdb=" O VAL H 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 75 through 77 Processing sheet with id=AC6, first strand: chain 'I' and resid 230 through 231 removed outlier: 4.051A pdb=" N SER I 169 " --> pdb=" O ILE I 231 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET I 166 " --> pdb=" O TYR I 276 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR I 278 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU I 168 " --> pdb=" O THR I 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 319 through 321 removed outlier: 3.631A pdb=" N ILE I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR I 326 " --> pdb=" O ILE I 345 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA I 344 " --> pdb=" O ILE I 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 331 through 333 Processing sheet with id=AC9, first strand: chain 'I' and resid 356 through 358 removed outlier: 6.572A pdb=" N LYS I 356 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE I 391 " --> pdb=" O ARG I 373 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N THR I 401 " --> pdb=" O ILE I 420 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP I 422 " --> pdb=" O THR I 401 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY I 403 " --> pdb=" O ASP I 422 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N MET I 424 " --> pdb=" O GLY I 403 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN I 405 " --> pdb=" O MET I 424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 378 through 379 removed outlier: 7.947A pdb=" N PHE I 378 " --> pdb=" O ILE I 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 104 through 108 removed outlier: 7.043A pdb=" N LEU J 27 " --> pdb=" O HIS J 73 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL J 75 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA J 29 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU J 77 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL J 31 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS J 79 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 133 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE J 235 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS J 167 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR J 274 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR J 165 " --> pdb=" O TYR J 274 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR J 276 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS J 167 " --> pdb=" O TYR J 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'J' and resid 318 through 321 removed outlier: 3.667A pdb=" N LYS J 327 " --> pdb=" O SER J 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR J 326 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 338 through 339 removed outlier: 7.872A pdb=" N LYS J 338 " --> pdb=" O ILE J 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 368 through 370 removed outlier: 7.043A pdb=" N ASN J 387 " --> pdb=" O GLY J 369 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 373 through 375 removed outlier: 3.928A pdb=" N LEU J 408 " --> pdb=" O ILE J 390 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG J 407 " --> pdb=" O LEU J 426 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 378 through 379 Processing sheet with id=AD9, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.705A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 31 through 35 Processing sheet with id=AE2, first strand: chain 'K' and resid 219 through 222 removed outlier: 3.914A pdb=" N LYS K 219 " --> pdb=" O THR K 231 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL K 229 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL K 188 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 230 " --> pdb=" O ALA K 186 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER K 191 " --> pdb=" O VAL K 261 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL K 261 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 19 through 23 removed outlier: 4.010A pdb=" N LYS L 35 " --> pdb=" O ASN L 23 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU L 47 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 227 through 233 removed outlier: 4.133A pdb=" N TYR L 228 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL L 188 " --> pdb=" O TYR L 228 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU L 230 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER L 191 " --> pdb=" O VAL L 261 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL L 261 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 141 through 149 removed outlier: 3.837A pdb=" N ARG M 187 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS M 149 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU M 185 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA M 99 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER M 190 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE M 101 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL M 192 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE M 103 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 314 through 321 removed outlier: 8.438A pdb=" N LEU M 315 " --> pdb=" O LEU M 343 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU M 343 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL M 317 " --> pdb=" O SER M 341 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER M 341 " --> pdb=" O VAL M 317 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY M 397 " --> pdb=" O LEU M 380 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU M 380 " --> pdb=" O GLY M 397 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY M 399 " --> pdb=" O VAL M 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 425 through 441 removed outlier: 4.054A pdb=" N ASN M 425 " --> pdb=" O THR M 493 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA M 491 " --> pdb=" O TYR M 427 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ASP M 429 " --> pdb=" O SER M 489 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N SER M 489 " --> pdb=" O ASP M 429 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N GLU M 431 " --> pdb=" O LEU M 487 " (cutoff:3.500A) removed outlier: 11.518A pdb=" N LEU M 487 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ASN M 433 " --> pdb=" O LEU M 485 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N LEU M 485 " --> pdb=" O ASN M 433 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE M 435 " --> pdb=" O ALA M 483 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N ALA M 483 " --> pdb=" O PHE M 435 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET M 482 " --> pdb=" O VAL M 478 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL M 478 " --> pdb=" O MET M 482 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR M 488 " --> pdb=" O GLY M 472 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY M 472 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA M 470 " --> pdb=" O PRO M 490 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR M 469 " --> pdb=" O ILE M 466 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ARG M 510 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N ARG M 439 " --> pdb=" O ARG M 510 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE M 512 " --> pdb=" O LEU M 437 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 141 through 149 removed outlier: 3.851A pdb=" N ALA N 143 " --> pdb=" O PHE N 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS N 149 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU N 185 " --> pdb=" O LYS N 149 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE N 103 " --> pdb=" O VAL N 192 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 314 through 320 removed outlier: 7.132A pdb=" N ARG N 314 " --> pdb=" O LEU N 343 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU N 343 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY N 339 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER N 320 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL N 337 " --> pdb=" O SER N 320 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY N 397 " --> pdb=" O LEU N 380 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU N 380 " --> pdb=" O GLY N 397 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY N 399 " --> pdb=" O VAL N 378 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 510 through 511 removed outlier: 4.357A pdb=" N LEU N 501 " --> pdb=" O GLY N 513 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY N 513 " --> pdb=" O LEU N 501 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP N 514 " --> pdb=" O PHE N 435 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N ILE N 426 " --> pdb=" O SER N 489 " (cutoff:3.500A) removed outlier: 12.960A pdb=" N SER N 489 " --> pdb=" O ILE N 426 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR N 428 " --> pdb=" O LEU N 487 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR N 488 " --> pdb=" O GLY N 472 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLY N 472 " --> pdb=" O THR N 488 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA N 470 " --> pdb=" O PRO N 490 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE N 466 " --> pdb=" O THR N 469 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN N 465 " --> pdb=" O ALA N 500 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 171 through 172 removed outlier: 4.212A pdb=" N VAL P 212 " --> pdb=" O SER P 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 204 " --> pdb=" O VAL P 212 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 244 through 245 1290 hydrogen bonds defined for protein. 3738 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: 8.33 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12514 1.34 - 1.48: 8591 1.48 - 1.61: 17936 1.61 - 1.75: 1 1.75 - 1.88: 262 Bond restraints: 39304 Sorted by residual: bond pdb=" CA VAL J 242 " pdb=" CB VAL J 242 " ideal model delta sigma weight residual 1.537 1.564 -0.028 5.00e-03 4.00e+04 3.03e+01 bond pdb=" CA GLY M 141 " pdb=" C GLY M 141 " ideal model delta sigma weight residual 1.518 1.557 -0.038 7.30e-03 1.88e+04 2.75e+01 bond pdb=" O1P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 39299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 49809 2.70 - 5.41: 3015 5.41 - 8.11: 315 8.11 - 10.81: 34 10.81 - 13.51: 4 Bond angle restraints: 53177 Sorted by residual: angle pdb=" C SER N 489 " pdb=" N PRO N 490 " pdb=" CA PRO N 490 " ideal model delta sigma weight residual 119.84 129.20 -9.36 1.25e+00 6.40e-01 5.61e+01 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 108.45 117.78 -9.33 1.26e+00 6.30e-01 5.48e+01 angle pdb=" C LEU I 97 " pdb=" N PRO I 98 " pdb=" CA PRO I 98 " ideal model delta sigma weight residual 119.84 128.84 -9.00 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N LYS M 300 " pdb=" CA LYS M 300 " pdb=" C LYS M 300 " ideal model delta sigma weight residual 110.97 118.75 -7.78 1.09e+00 8.42e-01 5.09e+01 angle pdb=" N VAL A 211 " pdb=" CA VAL A 211 " pdb=" C VAL A 211 " ideal model delta sigma weight residual 110.62 117.78 -7.16 1.02e+00 9.61e-01 4.92e+01 ... (remaining 53172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20199 17.67 - 35.34: 2824 35.34 - 53.01: 631 53.01 - 70.68: 338 70.68 - 88.35: 42 Dihedral angle restraints: 24034 sinusoidal: 9591 harmonic: 14443 Sorted by residual: dihedral pdb=" C ILE K 150 " pdb=" N ILE K 150 " pdb=" CA ILE K 150 " pdb=" CB ILE K 150 " ideal model delta harmonic sigma weight residual -122.00 -136.70 14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C ILE L 150 " pdb=" N ILE L 150 " pdb=" CA ILE L 150 " pdb=" CB ILE L 150 " ideal model delta harmonic sigma weight residual -122.00 -136.25 14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" N ILE K 150 " pdb=" C ILE K 150 " pdb=" CA ILE K 150 " pdb=" CB ILE K 150 " ideal model delta harmonic sigma weight residual 123.40 137.37 -13.97 0 2.50e+00 1.60e-01 3.12e+01 ... (remaining 24031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4908 0.099 - 0.198: 1028 0.198 - 0.297: 242 0.297 - 0.396: 42 0.396 - 0.495: 17 Chirality restraints: 6237 Sorted by residual: chirality pdb=" CA LEU J 202 " pdb=" N LEU J 202 " pdb=" C LEU J 202 " pdb=" CB LEU J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA ARG M 356 " pdb=" N ARG M 356 " pdb=" C ARG M 356 " pdb=" CB ARG M 356 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 6234 not shown) Planarity restraints: 6785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS M 139 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LYS M 139 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS M 139 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU M 140 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR I 304 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 305 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 305 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 305 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 157 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 158 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " -0.038 5.00e-02 4.00e+02 ... (remaining 6782 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 5 1.97 - 2.70: 249 2.70 - 3.43: 51014 3.43 - 4.17: 80197 4.17 - 4.90: 137678 Nonbonded interactions: 269143 Sorted by model distance: nonbonded pdb=" OG SER F 413 " pdb=" OE1 GLN F 414 " model vdw 1.236 3.040 nonbonded pdb=" OG SER F 413 " pdb=" CD GLN F 414 " model vdw 1.543 3.270 nonbonded pdb=" OD2 ASP B 17 " pdb=" NH1 ARG B 133 " model vdw 1.700 3.120 nonbonded pdb=" OG SER F 413 " pdb=" NE2 GLN F 414 " model vdw 1.775 3.120 nonbonded pdb=" ND2 ASN M 144 " pdb=" OE2 GLU M 383 " model vdw 1.777 3.120 ... (remaining 269138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.130 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.170 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3816 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 0.101 39304 Z= 0.603 Angle : 1.437 13.515 53177 Z= 0.943 Chirality : 0.090 0.495 6237 Planarity : 0.005 0.077 6785 Dihedral : 18.646 88.352 14636 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 3.41 % Allowed : 13.22 % Favored : 83.37 % Rotamer: Outliers : 7.64 % Allowed : 13.89 % Favored : 78.47 % Cbeta Deviations : 0.74 % 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 aren not related in a simple way. whole: -1.88 (0.11), residues: 4841 helix: 1.61 (0.12), residues: 1454 sheet: -0.47 (0.23), residues: 519 loop : -3.19 (0.10), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 301 TYR 0.021 0.002 TYR G 322 PHE 0.018 0.002 PHE C 51 TRP 0.011 0.001 TRP I 99 HIS 0.007 0.001 HIS H 415 Details of bonding type rmsd covalent geometry : bond 0.00851 (39304) covalent geometry : angle 1.43656 (53177) hydrogen bonds : bond 0.18413 ( 1282) hydrogen bonds : angle 7.30151 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 326 poor density : 582 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.3205 (OUTLIER) cc_final: 0.2443 (tpt170) REVERT: A 236 PHE cc_start: 0.1594 (OUTLIER) cc_final: 0.1276 (m-80) REVERT: C 238 ILE cc_start: 0.0582 (OUTLIER) cc_final: -0.0330 (mm) REVERT: C 260 ILE cc_start: 0.7679 (mt) cc_final: 0.7407 (mt) REVERT: C 310 GLU cc_start: 0.4119 (OUTLIER) cc_final: 0.2972 (mm-30) REVERT: C 312 PHE cc_start: 0.7941 (m-80) cc_final: 0.7282 (m-80) REVERT: D 31 ARG cc_start: 0.4375 (mtm180) cc_final: 0.3181 (mmt180) REVERT: D 104 MET cc_start: 0.0714 (mmt) cc_final: -0.0820 (mtt) REVERT: D 162 ILE cc_start: 0.7520 (mt) cc_final: 0.7246 (mm) REVERT: D 280 SER cc_start: 0.8888 (p) cc_final: 0.8654 (t) REVERT: E 144 ILE cc_start: 0.5066 (OUTLIER) cc_final: 0.4590 (tt) REVERT: F 141 ILE cc_start: -0.2074 (OUTLIER) cc_final: -0.2452 (pt) REVERT: F 222 PHE cc_start: -0.1778 (OUTLIER) cc_final: -0.2595 (m-80) REVERT: F 237 ILE cc_start: 0.6091 (mt) cc_final: 0.5794 (tp) REVERT: F 258 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: F 274 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5652 (m-40) REVERT: F 428 ILE cc_start: 0.2709 (mp) cc_final: 0.1802 (mm) REVERT: F 447 LYS cc_start: -0.3378 (mttt) cc_final: -0.4295 (tptp) REVERT: F 448 MET cc_start: 0.2392 (ttm) cc_final: 0.1461 (tpt) REVERT: F 457 ILE cc_start: 0.1217 (mt) cc_final: -0.0092 (tt) REVERT: F 467 LEU cc_start: -0.3009 (mp) cc_final: -0.3353 (mp) REVERT: F 512 ASN cc_start: 0.2544 (m-40) cc_final: 0.2061 (m-40) REVERT: F 521 ASN cc_start: 0.1230 (m-40) cc_final: 0.0255 (t0) REVERT: F 522 VAL cc_start: -0.4198 (t) cc_final: -0.4505 (p) REVERT: G 284 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.5474 (t80) REVERT: G 424 ILE cc_start: -0.0322 (OUTLIER) cc_final: -0.0906 (tt) REVERT: G 486 ARG cc_start: 0.5513 (mtm180) cc_final: 0.5005 (mpp80) REVERT: G 565 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4185 (mp) REVERT: H 324 SER cc_start: 0.8608 (m) cc_final: 0.8173 (t) REVERT: H 386 ILE cc_start: 0.6060 (mt) cc_final: 0.5794 (mt) REVERT: H 427 ILE cc_start: 0.8261 (mt) cc_final: 0.7465 (mp) REVERT: H 428 VAL cc_start: 0.8369 (t) cc_final: 0.8089 (p) REVERT: H 477 ILE cc_start: 0.2892 (OUTLIER) cc_final: 0.1770 (mt) REVERT: H 501 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5093 (pp) REVERT: H 530 ASN cc_start: 0.6456 (m-40) cc_final: 0.5692 (m-40) REVERT: J 65 GLU cc_start: 0.7843 (tt0) cc_final: 0.7599 (tt0) REVERT: J 163 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.5922 (mp) REVERT: J 173 THR cc_start: 0.7150 (OUTLIER) cc_final: 0.6897 (m) REVERT: J 274 TYR cc_start: 0.2933 (OUTLIER) cc_final: -0.1516 (m-80) REVERT: J 357 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8083 (tt) REVERT: K 64 ARG cc_start: -0.1833 (OUTLIER) cc_final: -0.2428 (mmt180) REVERT: L 33 TYR cc_start: 0.3215 (p90) cc_final: 0.1970 (p90) REVERT: L 54 ARG cc_start: 0.4070 (OUTLIER) cc_final: 0.2648 (mmt180) REVERT: M 204 MET cc_start: 0.2424 (tpt) cc_final: 0.1655 (tpp) REVERT: N 201 MET cc_start: -0.0432 (mmm) cc_final: -0.1273 (mmm) REVERT: N 211 MET cc_start: 0.1129 (mtp) cc_final: 0.0631 (mtm) REVERT: N 310 MET cc_start: 0.5960 (mmm) cc_final: 0.5375 (mmt) REVERT: N 489 SER cc_start: 0.4582 (OUTLIER) cc_final: 0.3676 (p) outliers start: 326 outliers final: 48 residues processed: 853 average time/residue: 0.2372 time to fit residues: 328.2196 Evaluate side-chains 397 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 328 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4249 > 50: distance: 31 - 35: 32.265 distance: 35 - 36: 50.425 distance: 36 - 37: 19.564 distance: 36 - 39: 31.851 distance: 37 - 38: 6.010 distance: 37 - 40: 4.751 distance: 40 - 41: 6.692 distance: 41 - 44: 5.625 distance: 42 - 49: 6.571 distance: 44 - 45: 4.945 distance: 46 - 47: 4.808 distance: 47 - 48: 3.423 distance: 49 - 50: 4.775 distance: 50 - 51: 12.671 distance: 50 - 53: 6.115 distance: 51 - 52: 10.160 distance: 51 - 56: 8.729 distance: 53 - 54: 6.297 distance: 53 - 55: 9.635 distance: 56 - 57: 5.290 distance: 57 - 58: 3.169 distance: 57 - 60: 4.680 distance: 58 - 59: 3.638 distance: 61 - 62: 4.503 distance: 62 - 63: 4.845 distance: 63 - 64: 4.994 distance: 68 - 71: 3.811 distance: 69 - 70: 10.041 distance: 71 - 72: 4.462 distance: 72 - 73: 3.308 distance: 74 - 75: 3.068 distance: 76 - 77: 12.104 distance: 77 - 78: 16.293 distance: 77 - 80: 9.721 distance: 78 - 79: 26.978 distance: 78 - 84: 13.559 distance: 80 - 81: 4.211 distance: 81 - 82: 14.059 distance: 81 - 83: 4.475 distance: 84 - 85: 5.942 distance: 85 - 86: 18.443 distance: 85 - 88: 8.991 distance: 86 - 87: 14.181 distance: 86 - 93: 16.606 distance: 89 - 90: 8.783 distance: 90 - 91: 3.249 distance: 90 - 92: 5.791 distance: 93 - 94: 12.035 distance: 93 - 99: 5.189 distance: 94 - 95: 18.361 distance: 94 - 97: 9.686 distance: 95 - 96: 23.187 distance: 95 - 100: 20.142 distance: 97 - 98: 5.426 distance: 98 - 99: 5.409 distance: 100 - 101: 7.651 distance: 101 - 102: 13.005 distance: 101 - 104: 12.577 distance: 102 - 103: 12.948 distance: 104 - 105: 3.108 distance: 105 - 106: 5.169 distance: 105 - 107: 6.270 distance: 108 - 109: 7.238 distance: 109 - 112: 4.024 distance: 110 - 117: 3.234 distance: 112 - 113: 4.461 distance: 114 - 116: 6.249