Starting phenix.real_space_refine on Thu Sep 26 14:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/09_2024/8oou_17031.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/09_2024/8oou_17031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/09_2024/8oou_17031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/09_2024/8oou_17031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/09_2024/8oou_17031.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/09_2024/8oou_17031.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 140 5.49 5 S 320 5.16 5 C 38620 2.51 5 N 10660 2.21 5 O 12060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61800 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "U" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Restraints were copied for chains: e, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 12.51, per 1000 atoms: 0.20 Number of scatterers: 61800 At special positions: 0 Unit cell: (186.635, 186.635, 175.185, 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 320 16.00 P 140 15.00 O 12060 8.00 N 10660 7.00 C 38620 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: 11.24 Conformation dependent library (CDL) restraints added in 10.8 seconds 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13920 Finding SS restraints... Secondary structure from input PDB file: 480 helices and 60 sheets defined 71.4% alpha, 5.3% beta 0 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 19.91 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE B 300 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 53 Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE C 220 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 143 Processing helix chain 'D' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE D 220 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE D 300 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 53 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE E 220 " --> pdb=" O HIS E 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE E 300 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 120 through 143 Processing helix chain 'F' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE F 160 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE F 220 " --> pdb=" O HIS F 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 248 Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU F 282 " --> pdb=" O GLN F 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE F 300 " --> pdb=" O GLU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER F 310 " --> pdb=" O PRO F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 331 Processing helix chain 'F' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 53 Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 143 Processing helix chain 'G' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE G 160 " --> pdb=" O CYS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 201 through 216 Processing helix chain 'G' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE G 220 " --> pdb=" O HIS G 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG G 259 " --> pdb=" O GLN G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE G 300 " --> pdb=" O GLU G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER G 310 " --> pdb=" O PRO G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 331 Processing helix chain 'G' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU G 359 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE G 378 " --> pdb=" O GLU G 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 143 Processing helix chain 'H' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE H 160 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 178 through 189 Processing helix chain 'H' and resid 190 through 197 Processing helix chain 'H' and resid 201 through 216 Processing helix chain 'H' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP H 221 " --> pdb=" O PRO H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG H 259 " --> pdb=" O GLN H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE H 300 " --> pdb=" O GLU H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER H 310 " --> pdb=" O PRO H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 331 Processing helix chain 'H' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 359 " --> pdb=" O GLU H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 53 Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 143 Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE I 160 " --> pdb=" O CYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 178 through 189 Processing helix chain 'I' and resid 190 through 197 Processing helix chain 'I' and resid 201 through 216 Processing helix chain 'I' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE I 220 " --> pdb=" O HIS I 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 221 " --> pdb=" O PRO I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 248 Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG I 259 " --> pdb=" O GLN I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU I 282 " --> pdb=" O GLN I 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE I 300 " --> pdb=" O GLU I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER I 310 " --> pdb=" O PRO I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 331 Processing helix chain 'I' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU I 359 " --> pdb=" O GLU I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 368 Processing helix chain 'I' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE I 378 " --> pdb=" O GLU I 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 53 Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 143 Processing helix chain 'J' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE J 160 " --> pdb=" O CYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 178 through 189 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 201 through 216 Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE J 220 " --> pdb=" O HIS J 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP J 221 " --> pdb=" O PRO J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 248 Processing helix chain 'J' and resid 249 through 251 No H-bonds generated for 'chain 'J' and resid 249 through 251' Processing helix chain 'J' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG J 259 " --> pdb=" O GLN J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU J 282 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE J 300 " --> pdb=" O GLU J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER J 310 " --> pdb=" O PRO J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 331 Processing helix chain 'J' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU J 359 " --> pdb=" O GLU J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 368 Processing helix chain 'J' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE J 378 " --> pdb=" O GLU J 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 9 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 53 Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 143 Processing helix chain 'K' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE K 160 " --> pdb=" O CYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 178 through 189 Processing helix chain 'K' and resid 190 through 197 Processing helix chain 'K' and resid 201 through 216 Processing helix chain 'K' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE K 220 " --> pdb=" O HIS K 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 248 Processing helix chain 'K' and resid 249 through 251 No H-bonds generated for 'chain 'K' and resid 249 through 251' Processing helix chain 'K' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG K 259 " --> pdb=" O GLN K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 273 Processing helix chain 'K' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE K 300 " --> pdb=" O GLU K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER K 310 " --> pdb=" O PRO K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 331 Processing helix chain 'K' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU K 359 " --> pdb=" O GLU K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 368 Processing helix chain 'K' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE K 378 " --> pdb=" O GLU K 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 40 through 53 Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 120 through 143 Processing helix chain 'L' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE L 160 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 178 through 189 Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'L' and resid 201 through 216 Processing helix chain 'L' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE L 220 " --> pdb=" O HIS L 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP L 221 " --> pdb=" O PRO L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 248 Processing helix chain 'L' and resid 249 through 251 No H-bonds generated for 'chain 'L' and resid 249 through 251' Processing helix chain 'L' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG L 259 " --> pdb=" O GLN L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU L 282 " --> pdb=" O GLN L 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN L 283 " --> pdb=" O ALA L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE L 300 " --> pdb=" O GLU L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER L 310 " --> pdb=" O PRO L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 331 Processing helix chain 'L' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU L 359 " --> pdb=" O GLU L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 364 through 368 Processing helix chain 'L' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE L 378 " --> pdb=" O GLU L 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 53 Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 143 Processing helix chain 'M' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE M 160 " --> pdb=" O CYS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 178 through 189 Processing helix chain 'M' and resid 190 through 197 Processing helix chain 'M' and resid 201 through 216 Processing helix chain 'M' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE M 220 " --> pdb=" O HIS M 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 248 Processing helix chain 'M' and resid 249 through 251 No H-bonds generated for 'chain 'M' and resid 249 through 251' Processing helix chain 'M' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU M 282 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN M 283 " --> pdb=" O ALA M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE M 300 " --> pdb=" O GLU M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER M 310 " --> pdb=" O PRO M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 331 Processing helix chain 'M' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS M 358 " --> pdb=" O ALA M 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'M' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE M 378 " --> pdb=" O GLU M 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 9 through 20 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 40 through 53 Processing helix chain 'N' and resid 61 through 75 Processing helix chain 'N' and resid 75 through 86 Processing helix chain 'N' and resid 120 through 143 Processing helix chain 'N' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE N 160 " --> pdb=" O CYS N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 178 through 189 Processing helix chain 'N' and resid 190 through 197 Processing helix chain 'N' and resid 201 through 216 Processing helix chain 'N' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE N 220 " --> pdb=" O HIS N 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP N 221 " --> pdb=" O PRO N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 248 Processing helix chain 'N' and resid 249 through 251 No H-bonds generated for 'chain 'N' and resid 249 through 251' Processing helix chain 'N' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG N 259 " --> pdb=" O GLN N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU N 282 " --> pdb=" O GLN N 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN N 283 " --> pdb=" O ALA N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER N 310 " --> pdb=" O PRO N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 331 Processing helix chain 'N' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS N 358 " --> pdb=" O ALA N 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU N 359 " --> pdb=" O GLU N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE N 378 " --> pdb=" O GLU N 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'O' and resid 9 through 20 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 40 through 53 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 120 through 143 Processing helix chain 'O' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE O 160 " --> pdb=" O CYS O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 178 through 189 Processing helix chain 'O' and resid 190 through 197 Processing helix chain 'O' and resid 201 through 216 Processing helix chain 'O' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE O 220 " --> pdb=" O HIS O 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP O 221 " --> pdb=" O PRO O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 248 Processing helix chain 'O' and resid 249 through 251 No H-bonds generated for 'chain 'O' and resid 249 through 251' Processing helix chain 'O' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG O 259 " --> pdb=" O GLN O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 273 Processing helix chain 'O' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU O 282 " --> pdb=" O GLN O 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN O 283 " --> pdb=" O ALA O 279 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE O 300 " --> pdb=" O GLU O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER O 310 " --> pdb=" O PRO O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 331 Processing helix chain 'O' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS O 358 " --> pdb=" O ALA O 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU O 359 " --> pdb=" O GLU O 355 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 368 Processing helix chain 'O' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE O 378 " --> pdb=" O GLU O 374 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 6 Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 143 Processing helix chain 'P' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE P 160 " --> pdb=" O CYS P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 178 through 189 Processing helix chain 'P' and resid 190 through 197 Processing helix chain 'P' and resid 201 through 216 Processing helix chain 'P' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE P 220 " --> pdb=" O HIS P 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP P 221 " --> pdb=" O PRO P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 248 Processing helix chain 'P' and resid 249 through 251 No H-bonds generated for 'chain 'P' and resid 249 through 251' Processing helix chain 'P' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 273 Processing helix chain 'P' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU P 282 " --> pdb=" O GLN P 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN P 283 " --> pdb=" O ALA P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE P 300 " --> pdb=" O GLU P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER P 310 " --> pdb=" O PRO P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 331 Processing helix chain 'P' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS P 358 " --> pdb=" O ALA P 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU P 359 " --> pdb=" O GLU P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 368 Processing helix chain 'P' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE P 378 " --> pdb=" O GLU P 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 9 through 20 Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 53 Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 143 Processing helix chain 'Q' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE Q 160 " --> pdb=" O CYS Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 178 through 189 Processing helix chain 'Q' and resid 190 through 197 Processing helix chain 'Q' and resid 201 through 216 Processing helix chain 'Q' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE Q 220 " --> pdb=" O HIS Q 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP Q 221 " --> pdb=" O PRO Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 248 Processing helix chain 'Q' and resid 249 through 251 No H-bonds generated for 'chain 'Q' and resid 249 through 251' Processing helix chain 'Q' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG Q 259 " --> pdb=" O GLN Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 269 through 273 Processing helix chain 'Q' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU Q 282 " --> pdb=" O GLN Q 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN Q 283 " --> pdb=" O ALA Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE Q 300 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER Q 310 " --> pdb=" O PRO Q 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 331 Processing helix chain 'Q' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS Q 358 " --> pdb=" O ALA Q 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU Q 359 " --> pdb=" O GLU Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 368 Processing helix chain 'Q' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE Q 378 " --> pdb=" O GLU Q 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 6 Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 37 through 39 No H-bonds generated for 'chain 'R' and resid 37 through 39' Processing helix chain 'R' and resid 40 through 53 Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 120 through 143 Processing helix chain 'R' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE R 160 " --> pdb=" O CYS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 178 through 189 Processing helix chain 'R' and resid 190 through 197 Processing helix chain 'R' and resid 201 through 216 Processing helix chain 'R' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP R 221 " --> pdb=" O PRO R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 248 Processing helix chain 'R' and resid 249 through 251 No H-bonds generated for 'chain 'R' and resid 249 through 251' Processing helix chain 'R' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG R 259 " --> pdb=" O GLN R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 273 Processing helix chain 'R' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU R 282 " --> pdb=" O GLN R 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE R 300 " --> pdb=" O GLU R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER R 310 " --> pdb=" O PRO R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 331 Processing helix chain 'R' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS R 358 " --> pdb=" O ALA R 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU R 359 " --> pdb=" O GLU R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE R 378 " --> pdb=" O GLU R 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 53 Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 143 Processing helix chain 'S' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE S 160 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 178 through 189 Processing helix chain 'S' and resid 190 through 197 Processing helix chain 'S' and resid 201 through 216 Processing helix chain 'S' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE S 220 " --> pdb=" O HIS S 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP S 221 " --> pdb=" O PRO S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 248 Processing helix chain 'S' and resid 249 through 251 No H-bonds generated for 'chain 'S' and resid 249 through 251' Processing helix chain 'S' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG S 259 " --> pdb=" O GLN S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'S' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU S 282 " --> pdb=" O GLN S 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN S 283 " --> pdb=" O ALA S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE S 300 " --> pdb=" O GLU S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER S 310 " --> pdb=" O PRO S 307 " (cutoff:3.500A) Processing helix chain 'S' and resid 317 through 331 Processing helix chain 'S' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS S 358 " --> pdb=" O ALA S 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU S 359 " --> pdb=" O GLU S 355 " (cutoff:3.500A) Processing helix chain 'S' and resid 364 through 368 Processing helix chain 'S' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE S 378 " --> pdb=" O GLU S 374 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 6 Processing helix chain 'T' and resid 9 through 20 Processing helix chain 'T' and resid 37 through 39 No H-bonds generated for 'chain 'T' and resid 37 through 39' Processing helix chain 'T' and resid 40 through 53 Processing helix chain 'T' and resid 61 through 75 Processing helix chain 'T' and resid 75 through 86 Processing helix chain 'T' and resid 120 through 143 Processing helix chain 'T' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE T 160 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 174 No H-bonds generated for 'chain 'T' and resid 172 through 174' Processing helix chain 'T' and resid 178 through 189 Processing helix chain 'T' and resid 190 through 197 Processing helix chain 'T' and resid 201 through 216 Processing helix chain 'T' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP T 221 " --> pdb=" O PRO T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 248 Processing helix chain 'T' and resid 249 through 251 No H-bonds generated for 'chain 'T' and resid 249 through 251' Processing helix chain 'T' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG T 259 " --> pdb=" O GLN T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 273 Processing helix chain 'T' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU T 282 " --> pdb=" O GLN T 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN T 283 " --> pdb=" O ALA T 279 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE T 300 " --> pdb=" O GLU T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER T 310 " --> pdb=" O PRO T 307 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 331 Processing helix chain 'T' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS T 358 " --> pdb=" O ALA T 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU T 359 " --> pdb=" O GLU T 355 " (cutoff:3.500A) Processing helix chain 'T' and resid 364 through 368 Processing helix chain 'T' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE T 378 " --> pdb=" O GLU T 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE A 33 " --> pdb=" O ASN A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE B 33 " --> pdb=" O ASN B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 104 Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG C 27 " --> pdb=" O HIS C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE C 33 " --> pdb=" O ASN C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 104 Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG D 27 " --> pdb=" O HIS D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE D 33 " --> pdb=" O ASN D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 97 through 104 Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG E 27 " --> pdb=" O HIS E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE E 33 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 97 through 104 Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG F 27 " --> pdb=" O HIS F 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE F 33 " --> pdb=" O ASN F 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 97 through 104 Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG G 27 " --> pdb=" O HIS G 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE G 33 " --> pdb=" O ASN G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 97 through 104 Processing sheet with id=AC4, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG H 27 " --> pdb=" O HIS H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE H 33 " --> pdb=" O ASN H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 97 through 104 Processing sheet with id=AC7, first strand: chain 'I' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG I 27 " --> pdb=" O HIS I 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE I 33 " --> pdb=" O ASN I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 97 through 104 Processing sheet with id=AD1, first strand: chain 'J' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG J 27 " --> pdb=" O HIS J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE J 33 " --> pdb=" O ASN J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 97 through 104 Processing sheet with id=AD4, first strand: chain 'K' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG K 27 " --> pdb=" O HIS K 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE K 33 " --> pdb=" O ASN K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 97 through 104 Processing sheet with id=AD7, first strand: chain 'L' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG L 27 " --> pdb=" O HIS L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'L' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE L 33 " --> pdb=" O ASN L 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'L' and resid 97 through 104 Processing sheet with id=AE1, first strand: chain 'M' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG M 27 " --> pdb=" O HIS M 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'M' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE M 33 " --> pdb=" O ASN M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 97 through 104 Processing sheet with id=AE4, first strand: chain 'N' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG N 27 " --> pdb=" O HIS N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE N 33 " --> pdb=" O ASN N 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'N' and resid 97 through 104 Processing sheet with id=AE7, first strand: chain 'O' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG O 27 " --> pdb=" O HIS O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'O' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE O 33 " --> pdb=" O ASN O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 97 through 104 Processing sheet with id=AF1, first strand: chain 'P' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG P 27 " --> pdb=" O HIS P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE P 33 " --> pdb=" O ASN P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'P' and resid 97 through 104 Processing sheet with id=AF4, first strand: chain 'Q' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG Q 27 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'Q' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE Q 33 " --> pdb=" O ASN Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Q' and resid 97 through 104 Processing sheet with id=AF7, first strand: chain 'R' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG R 27 " --> pdb=" O HIS R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'R' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE R 33 " --> pdb=" O ASN R 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'R' and resid 97 through 104 Processing sheet with id=AG1, first strand: chain 'S' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG S 27 " --> pdb=" O HIS S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'S' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE S 33 " --> pdb=" O ASN S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'S' and resid 97 through 104 Processing sheet with id=AG4, first strand: chain 'T' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG T 27 " --> pdb=" O HIS T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'T' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE T 33 " --> pdb=" O ASN T 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'T' and resid 97 through 104 3580 hydrogen bonds defined for protein. 9940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 28.41 Time building geometry restraints manager: 13.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 62048 1.54 - 1.86: 1012 1.86 - 2.18: 0 2.18 - 2.50: 0 2.50 - 2.82: 18 Bond restraints: 63078 Sorted by residual: bond pdb=" O3' C U1014 " pdb=" P C U1015 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1014 " pdb=" P C e1015 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C U1049 " pdb=" P C U1050 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1049 " pdb=" P C e1050 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1007 " pdb=" P C e1008 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.51e+03 ... (remaining 63073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.60: 85558 8.60 - 17.19: 0 17.19 - 25.79: 18 25.79 - 34.39: 18 34.39 - 42.99: 18 Bond angle restraints: 85612 Sorted by residual: angle pdb=" O3' C e1014 " pdb=" P C e1015 " pdb=" O5' C e1015 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C U1014 " pdb=" P C U1015 " pdb=" O5' C U1015 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C U1049 " pdb=" P C U1050 " pdb=" O5' C U1050 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C e1049 " pdb=" P C e1050 " pdb=" O5' C e1050 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C e1028 " pdb=" P C e1029 " pdb=" O5' C e1029 " ideal model delta sigma weight residual 104.00 75.64 28.36 1.50e+00 4.44e-01 3.57e+02 ... (remaining 85607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 35058 17.76 - 35.53: 2776 35.53 - 53.29: 400 53.29 - 71.05: 160 71.05 - 88.81: 180 Dihedral angle restraints: 38574 sinusoidal: 16754 harmonic: 21820 Sorted by residual: dihedral pdb=" CA ARG O 338 " pdb=" C ARG O 338 " pdb=" N GLY O 339 " pdb=" CA GLY O 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG T 338 " pdb=" C ARG T 338 " pdb=" N GLY T 339 " pdb=" CA GLY T 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG E 338 " pdb=" C ARG E 338 " pdb=" N GLY E 339 " pdb=" CA GLY E 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 38571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 5780 0.034 - 0.069: 2960 0.069 - 0.103: 740 0.103 - 0.137: 320 0.137 - 0.172: 20 Chirality restraints: 9820 Sorted by residual: chirality pdb=" CB VAL S 284 " pdb=" CA VAL S 284 " pdb=" CG1 VAL S 284 " pdb=" CG2 VAL S 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL N 284 " pdb=" CA VAL N 284 " pdb=" CG1 VAL N 284 " pdb=" CG2 VAL N 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL D 284 " pdb=" CA VAL D 284 " pdb=" CG1 VAL D 284 " pdb=" CG2 VAL D 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 9817 not shown) Planarity restraints: 10520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 149 " 0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR L 149 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR L 149 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR L 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR L 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR L 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 149 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 149 " -0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR G 149 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR G 149 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR G 149 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR G 149 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR G 149 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 149 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 149 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 149 " 0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR B 149 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 149 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 149 " 0.002 2.00e-02 2.50e+03 ... (remaining 10517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7168 2.74 - 3.28: 60942 3.28 - 3.82: 104240 3.82 - 4.36: 134256 4.36 - 4.90: 217416 Nonbonded interactions: 524022 Sorted by model distance: nonbonded pdb=" OE1 GLU G 297 " pdb=" OH TYR G 301 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU L 297 " pdb=" OH TYR L 301 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR B 301 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU Q 297 " pdb=" OH TYR Q 301 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU J 297 " pdb=" OH TYR J 301 " model vdw 2.204 3.040 ... (remaining 524017 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' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'B' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'C' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'D' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'E' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'F' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'G' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'H' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'I' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'J' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'K' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'L' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'M' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'N' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'O' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'P' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'Q' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'R' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'S' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'T' and (resid 2 through 99 or resid 101 through 379)) } ncs_group { reference = chain 'U' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.850 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: 0.080 Extract box with map and model: 1.720 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 120.910 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.021 1.211 63078 Z= 1.282 Angle : 1.033 42.987 85612 Z= 0.504 Chirality : 0.044 0.172 9820 Planarity : 0.003 0.034 10520 Dihedral : 14.494 88.812 24654 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 7540 helix: 0.86 (0.07), residues: 4720 sheet: 0.74 (0.22), residues: 440 loop : -0.15 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 260 HIS 0.006 0.001 HIS E 225 PHE 0.019 0.002 PHE S 219 TYR 0.022 0.002 TYR G 149 ARG 0.004 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 5.069 Fit side-chains REVERT: A 71 MET cc_start: 0.9205 (mtm) cc_final: 0.8963 (mtp) REVERT: B 50 MET cc_start: 0.9065 (mtm) cc_final: 0.8863 (mtm) REVERT: B 71 MET cc_start: 0.9158 (mtm) cc_final: 0.8768 (mtp) REVERT: C 64 LEU cc_start: 0.8985 (tt) cc_final: 0.8717 (tm) REVERT: E 71 MET cc_start: 0.9221 (mtm) cc_final: 0.8875 (mtp) REVERT: E 158 MET cc_start: 0.8922 (mmm) cc_final: 0.8718 (mmp) REVERT: E 343 ASN cc_start: 0.8234 (t0) cc_final: 0.7958 (t0) REVERT: F 71 MET cc_start: 0.9206 (mtm) cc_final: 0.8962 (mtp) REVERT: G 50 MET cc_start: 0.9066 (mtm) cc_final: 0.8863 (mtm) REVERT: G 71 MET cc_start: 0.9159 (mtm) cc_final: 0.8769 (mtp) REVERT: H 64 LEU cc_start: 0.8987 (tt) cc_final: 0.8717 (tm) REVERT: J 71 MET cc_start: 0.9221 (mtm) cc_final: 0.8877 (mtp) REVERT: J 158 MET cc_start: 0.8923 (mmm) cc_final: 0.8718 (mmp) REVERT: J 343 ASN cc_start: 0.8238 (t0) cc_final: 0.7958 (t0) REVERT: K 71 MET cc_start: 0.9209 (mtm) cc_final: 0.8967 (mtp) REVERT: L 50 MET cc_start: 0.9064 (mtm) cc_final: 0.8863 (mtm) REVERT: L 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8770 (mtp) REVERT: M 64 LEU cc_start: 0.8989 (tt) cc_final: 0.8715 (tm) REVERT: O 71 MET cc_start: 0.9217 (mtm) cc_final: 0.8877 (mtp) REVERT: O 158 MET cc_start: 0.8925 (mmm) cc_final: 0.8722 (mmp) REVERT: O 343 ASN cc_start: 0.8238 (t0) cc_final: 0.7956 (t0) REVERT: P 71 MET cc_start: 0.9203 (mtm) cc_final: 0.8959 (mtp) REVERT: Q 50 MET cc_start: 0.9064 (mtm) cc_final: 0.8862 (mtm) REVERT: Q 71 MET cc_start: 0.9164 (mtm) cc_final: 0.8779 (mtp) REVERT: R 64 LEU cc_start: 0.8989 (tt) cc_final: 0.8718 (tm) REVERT: T 71 MET cc_start: 0.9219 (mtm) cc_final: 0.8875 (mtp) REVERT: T 158 MET cc_start: 0.8925 (mmm) cc_final: 0.8721 (mmp) REVERT: T 343 ASN cc_start: 0.8238 (t0) cc_final: 0.7957 (t0) outliers start: 0 outliers final: 4 residues processed: 980 average time/residue: 1.8435 time to fit residues: 2204.4468 Evaluate side-chains 788 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 784 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain P residue 96 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 636 optimal weight: 0.5980 chunk 571 optimal weight: 0.6980 chunk 317 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 385 optimal weight: 0.5980 chunk 305 optimal weight: 1.9990 chunk 590 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 359 optimal weight: 0.5980 chunk 439 optimal weight: 0.8980 chunk 684 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 89 HIS ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 89 HIS ** B 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN D 26 GLN D 89 HIS ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN E 26 GLN E 89 HIS F 26 GLN F 89 HIS ** F 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 89 HIS ** G 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 GLN I 26 GLN I 89 HIS ** I 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN J 26 GLN J 89 HIS K 26 GLN K 89 HIS L 26 GLN L 89 HIS ** L 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 356 GLN N 26 GLN N 89 HIS ** N 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN O 26 GLN O 89 HIS P 26 GLN P 89 HIS ** P 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN Q 89 HIS ** Q 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 356 GLN S 26 GLN S 89 HIS ** S 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN T 26 GLN T 89 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63078 Z= 0.198 Angle : 0.530 5.441 85612 Z= 0.288 Chirality : 0.041 0.165 9820 Planarity : 0.004 0.053 10520 Dihedral : 11.320 73.985 10462 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.59 % Allowed : 8.67 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 7540 helix: 1.32 (0.07), residues: 4720 sheet: 0.94 (0.25), residues: 300 loop : 0.16 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 260 HIS 0.005 0.001 HIS N 225 PHE 0.011 0.002 PHE G 219 TYR 0.010 0.001 TYR F 337 ARG 0.011 0.001 ARG J 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 844 time to evaluate : 5.057 Fit side-chains REVERT: A 366 SER cc_start: 0.8441 (m) cc_final: 0.8187 (p) REVERT: B 71 MET cc_start: 0.9186 (mtm) cc_final: 0.8804 (mtp) REVERT: B 192 ASN cc_start: 0.8434 (m110) cc_final: 0.8165 (m-40) REVERT: B 248 MET cc_start: 0.7802 (mmp) cc_final: 0.7497 (mmp) REVERT: B 271 MET cc_start: 0.8367 (mmm) cc_final: 0.7834 (mmm) REVERT: B 366 SER cc_start: 0.8345 (m) cc_final: 0.8011 (p) REVERT: C 55 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7016 (pm20) REVERT: C 64 LEU cc_start: 0.8970 (tt) cc_final: 0.8647 (tm) REVERT: C 336 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7182 (pt0) REVERT: C 342 ARG cc_start: 0.7599 (ptp-110) cc_final: 0.7249 (ptm160) REVERT: D 342 ARG cc_start: 0.7528 (ptp-110) cc_final: 0.7310 (ptm160) REVERT: E 71 MET cc_start: 0.9291 (mtm) cc_final: 0.8958 (mtp) REVERT: E 77 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7254 (mm-30) REVERT: E 122 GLU cc_start: 0.7699 (mp0) cc_final: 0.7327 (mp0) REVERT: E 342 ARG cc_start: 0.7329 (ptp-110) cc_final: 0.7041 (ptp-170) REVERT: F 366 SER cc_start: 0.8444 (m) cc_final: 0.8184 (p) REVERT: G 71 MET cc_start: 0.9190 (mtm) cc_final: 0.8806 (mtp) REVERT: G 192 ASN cc_start: 0.8426 (m110) cc_final: 0.8157 (m-40) REVERT: G 248 MET cc_start: 0.7804 (mmp) cc_final: 0.7499 (mmp) REVERT: G 271 MET cc_start: 0.8365 (mmm) cc_final: 0.7830 (mmm) REVERT: G 366 SER cc_start: 0.8346 (m) cc_final: 0.8011 (p) REVERT: H 55 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: H 64 LEU cc_start: 0.8973 (tt) cc_final: 0.8649 (tm) REVERT: H 336 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7183 (pt0) REVERT: H 342 ARG cc_start: 0.7597 (ptp-110) cc_final: 0.7248 (ptm160) REVERT: I 342 ARG cc_start: 0.7526 (ptp-110) cc_final: 0.7308 (ptm160) REVERT: J 71 MET cc_start: 0.9291 (mtm) cc_final: 0.8968 (mtp) REVERT: J 122 GLU cc_start: 0.7701 (mp0) cc_final: 0.7334 (mp0) REVERT: J 342 ARG cc_start: 0.7331 (ptp-110) cc_final: 0.7040 (ptp-170) REVERT: K 366 SER cc_start: 0.8444 (m) cc_final: 0.8188 (p) REVERT: L 71 MET cc_start: 0.9193 (mtm) cc_final: 0.8812 (mtp) REVERT: L 192 ASN cc_start: 0.8434 (m110) cc_final: 0.8167 (m-40) REVERT: L 248 MET cc_start: 0.7800 (mmp) cc_final: 0.7493 (mmp) REVERT: L 271 MET cc_start: 0.8365 (mmm) cc_final: 0.7830 (mmm) REVERT: L 366 SER cc_start: 0.8350 (m) cc_final: 0.8014 (p) REVERT: M 55 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: M 64 LEU cc_start: 0.8974 (tt) cc_final: 0.8646 (tm) REVERT: M 336 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7186 (pt0) REVERT: M 342 ARG cc_start: 0.7595 (ptp-110) cc_final: 0.7248 (ptm160) REVERT: N 342 ARG cc_start: 0.7523 (ptp-110) cc_final: 0.7307 (ptm160) REVERT: O 71 MET cc_start: 0.9289 (mtm) cc_final: 0.8963 (mtp) REVERT: O 77 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7257 (mm-30) REVERT: O 122 GLU cc_start: 0.7693 (mp0) cc_final: 0.7328 (mp0) REVERT: O 342 ARG cc_start: 0.7327 (ptp-110) cc_final: 0.7032 (ptp-170) REVERT: P 366 SER cc_start: 0.8441 (m) cc_final: 0.8183 (p) REVERT: Q 50 MET cc_start: 0.9019 (mtm) cc_final: 0.8818 (mtm) REVERT: Q 71 MET cc_start: 0.9191 (mtm) cc_final: 0.8814 (mtp) REVERT: Q 192 ASN cc_start: 0.8429 (m110) cc_final: 0.8160 (m-40) REVERT: Q 248 MET cc_start: 0.7798 (mmp) cc_final: 0.7493 (mmp) REVERT: Q 271 MET cc_start: 0.8362 (mmm) cc_final: 0.7827 (mmm) REVERT: Q 366 SER cc_start: 0.8353 (m) cc_final: 0.8015 (p) REVERT: R 55 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: R 64 LEU cc_start: 0.8975 (tt) cc_final: 0.8651 (tm) REVERT: R 336 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7185 (pt0) REVERT: R 342 ARG cc_start: 0.7602 (ptp-110) cc_final: 0.7251 (ptm160) REVERT: S 130 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7331 (mm-30) REVERT: S 342 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.7306 (ptm160) REVERT: T 71 MET cc_start: 0.9291 (mtm) cc_final: 0.8966 (mtp) REVERT: T 122 GLU cc_start: 0.7694 (mp0) cc_final: 0.7332 (mp0) REVERT: T 342 ARG cc_start: 0.7329 (ptp-110) cc_final: 0.7038 (ptp-170) outliers start: 164 outliers final: 72 residues processed: 940 average time/residue: 1.7368 time to fit residues: 2007.2718 Evaluate side-chains 841 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 765 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3265 > 50: distance: 68 - 86: 10.774 distance: 84 - 86: 11.733 distance: 86 - 87: 22.538 distance: 87 - 88: 9.954 distance: 87 - 90: 20.856 distance: 88 - 89: 10.145 distance: 88 - 94: 19.637 distance: 90 - 91: 44.507 distance: 91 - 92: 36.992 distance: 91 - 93: 26.921 distance: 94 - 95: 56.360 distance: 95 - 96: 6.825 distance: 96 - 97: 30.096 distance: 96 - 98: 21.663 distance: 98 - 99: 15.223 distance: 99 - 100: 29.874 distance: 99 - 102: 13.111 distance: 100 - 101: 31.483 distance: 100 - 106: 24.978 distance: 102 - 103: 34.530 distance: 102 - 104: 32.852 distance: 103 - 105: 13.052 distance: 106 - 107: 11.683 distance: 107 - 108: 25.667 distance: 107 - 110: 15.667 distance: 108 - 109: 27.925 distance: 108 - 114: 34.308 distance: 110 - 111: 22.535 distance: 111 - 112: 25.771 distance: 112 - 113: 35.484 distance: 114 - 115: 36.356 distance: 115 - 116: 6.069 distance: 116 - 117: 31.856 distance: 116 - 118: 7.494 distance: 118 - 119: 16.360 distance: 119 - 120: 7.847 distance: 119 - 122: 16.348 distance: 120 - 121: 6.857 distance: 120 - 127: 9.704 distance: 122 - 123: 10.667 distance: 123 - 124: 9.619 distance: 124 - 125: 7.631 distance: 124 - 126: 5.454 distance: 127 - 128: 16.143 distance: 128 - 129: 17.213 distance: 128 - 131: 29.810 distance: 129 - 130: 17.762 distance: 129 - 139: 23.097 distance: 131 - 132: 16.221 distance: 132 - 133: 12.978 distance: 132 - 134: 21.971 distance: 133 - 135: 25.845 distance: 134 - 136: 20.644 distance: 135 - 137: 37.057 distance: 136 - 137: 20.519 distance: 137 - 138: 15.358 distance: 139 - 140: 12.693 distance: 140 - 141: 17.607 distance: 140 - 143: 17.912 distance: 141 - 142: 35.592 distance: 141 - 150: 13.296 distance: 143 - 144: 21.484 distance: 144 - 145: 16.522 distance: 145 - 146: 16.655 distance: 146 - 147: 20.056 distance: 147 - 148: 9.339 distance: 147 - 149: 15.107 distance: 150 - 151: 28.377 distance: 151 - 152: 18.726 distance: 152 - 153: 23.930 distance: 152 - 154: 20.222 distance: 154 - 155: 23.329 distance: 155 - 156: 14.568 distance: 155 - 158: 15.776 distance: 156 - 157: 17.765 distance: 156 - 161: 17.663 distance: 158 - 159: 18.602 distance: 158 - 160: 36.368