Starting phenix.real_space_refine on Mon Dec 30 07:14:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oou_17031/12_2024/8oou_17031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oou_17031/12_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/cci-nas-00/data/ceres_data/8oou_17031/12_2024/8oou_17031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oou_17031/12_2024/8oou_17031.map" model { file = "/net/cci-nas-00/data/ceres_data/8oou_17031/12_2024/8oou_17031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oou_17031/12_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-5532/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: 12.31, 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: 13.02 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: 15.86 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: 24.56 Time building geometry restraints manager: 15.22 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.750 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 111.540 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.430 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 980 time to evaluate : 5.199 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: 1.7904 time to fit residues: 2143.6316 Evaluate side-chains 788 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 784 time to evaluate : 5.068 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 164 poor density : 844 time to evaluate : 5.146 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: 0.8959 (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: 1.7475 time to fit residues: 2015.2975 Evaluate side-chains 841 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 765 time to evaluate : 5.082 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 754 random chunks: chunk 380 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 569 optimal weight: 4.9990 chunk 466 optimal weight: 3.9990 chunk 188 optimal weight: 0.0020 chunk 685 optimal weight: 3.9990 chunk 741 optimal weight: 1.9990 chunk 610 optimal weight: 0.6980 chunk 680 optimal weight: 0.9990 chunk 233 optimal weight: 0.5980 chunk 550 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN D 26 GLN D 89 HIS ** D 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN E 45 ASN E 89 HIS F 89 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN I 26 GLN I 89 HIS ** I 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN J 89 HIS K 89 HIS ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 26 GLN N 89 HIS ** N 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 HIS P 89 HIS ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 102 GLN S 26 GLN S 89 HIS ** S 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN T 89 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 63078 Z= 0.170 Angle : 0.490 6.191 85612 Z= 0.263 Chirality : 0.039 0.146 9820 Planarity : 0.004 0.044 10520 Dihedral : 11.111 73.802 10454 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.22 % Allowed : 11.47 % Favored : 86.31 % 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: 1.59 (0.10), residues: 7540 helix: 1.51 (0.07), residues: 4720 sheet: 1.10 (0.26), residues: 300 loop : 0.32 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 260 HIS 0.004 0.001 HIS F 225 PHE 0.009 0.002 PHE R 226 TYR 0.011 0.001 TYR J 337 ARG 0.009 0.001 ARG J 338 *********************** REFINEMENT MACRO_CYCLE 3 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 958 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 818 time to evaluate : 5.118 Fit side-chains REVERT: A 55 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6487 (pm20) REVERT: A 67 MET cc_start: 0.8747 (mmm) cc_final: 0.8487 (mmm) REVERT: A 77 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 192 ASN cc_start: 0.8445 (m110) cc_final: 0.8172 (m-40) REVERT: B 271 MET cc_start: 0.8349 (mmm) cc_final: 0.7827 (mmm) REVERT: B 292 GLN cc_start: 0.8130 (pt0) cc_final: 0.7841 (mt0) REVERT: B 366 SER cc_start: 0.8332 (m) cc_final: 0.8021 (p) REVERT: C 64 LEU cc_start: 0.8941 (tt) cc_final: 0.8610 (tm) REVERT: C 130 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7240 (mp0) REVERT: D 194 MET cc_start: 0.8595 (mtm) cc_final: 0.7892 (mtm) REVERT: D 342 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7322 (ptm160) REVERT: E 55 GLU cc_start: 0.7261 (pt0) cc_final: 0.7018 (pm20) REVERT: E 71 MET cc_start: 0.9257 (mtm) cc_final: 0.8925 (mtp) REVERT: E 77 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7298 (mm-30) REVERT: E 283 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: E 342 ARG cc_start: 0.7355 (ptp-110) cc_final: 0.7130 (ptp-110) REVERT: F 55 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: F 67 MET cc_start: 0.8745 (mmm) cc_final: 0.8486 (mmm) REVERT: F 77 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7323 (mm-30) REVERT: G 192 ASN cc_start: 0.8438 (m110) cc_final: 0.8165 (m-40) REVERT: G 271 MET cc_start: 0.8346 (mmm) cc_final: 0.7823 (mmm) REVERT: G 292 GLN cc_start: 0.8140 (pt0) cc_final: 0.7847 (mt0) REVERT: G 366 SER cc_start: 0.8334 (m) cc_final: 0.8020 (p) REVERT: H 64 LEU cc_start: 0.8945 (tt) cc_final: 0.8611 (tm) REVERT: H 130 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7244 (mp0) REVERT: I 194 MET cc_start: 0.8599 (mtm) cc_final: 0.7898 (mtm) REVERT: I 342 ARG cc_start: 0.7536 (ptp-110) cc_final: 0.7323 (ptm160) REVERT: J 55 GLU cc_start: 0.7265 (pt0) cc_final: 0.7025 (pm20) REVERT: J 71 MET cc_start: 0.9257 (mtm) cc_final: 0.8930 (mtp) REVERT: J 283 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: J 342 ARG cc_start: 0.7358 (ptp-110) cc_final: 0.7136 (ptp-110) REVERT: K 55 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: K 67 MET cc_start: 0.8749 (mmm) cc_final: 0.8483 (mmm) REVERT: K 77 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7325 (mm-30) REVERT: L 192 ASN cc_start: 0.8447 (m110) cc_final: 0.8174 (m-40) REVERT: L 271 MET cc_start: 0.8346 (mmm) cc_final: 0.7826 (mmm) REVERT: L 292 GLN cc_start: 0.8126 (pt0) cc_final: 0.7838 (mt0) REVERT: L 366 SER cc_start: 0.8337 (m) cc_final: 0.8023 (p) REVERT: M 64 LEU cc_start: 0.8944 (tt) cc_final: 0.8609 (tm) REVERT: M 130 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7237 (mp0) REVERT: N 194 MET cc_start: 0.8596 (mtm) cc_final: 0.7894 (mtm) REVERT: N 342 ARG cc_start: 0.7532 (ptp-110) cc_final: 0.7320 (ptm160) REVERT: O 55 GLU cc_start: 0.7260 (pt0) cc_final: 0.7017 (pm20) REVERT: O 71 MET cc_start: 0.9255 (mtm) cc_final: 0.8928 (mtp) REVERT: O 77 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7301 (mm-30) REVERT: O 283 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: O 342 ARG cc_start: 0.7360 (ptp-110) cc_final: 0.7138 (ptp-110) REVERT: P 55 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: P 67 MET cc_start: 0.8738 (mmm) cc_final: 0.8481 (mmm) REVERT: P 77 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7318 (mm-30) REVERT: Q 50 MET cc_start: 0.9006 (mtm) cc_final: 0.8805 (mtm) REVERT: Q 192 ASN cc_start: 0.8440 (m110) cc_final: 0.8168 (m-40) REVERT: Q 271 MET cc_start: 0.8344 (mmm) cc_final: 0.7822 (mmm) REVERT: Q 292 GLN cc_start: 0.8143 (pt0) cc_final: 0.7849 (mt0) REVERT: Q 366 SER cc_start: 0.8339 (m) cc_final: 0.8025 (p) REVERT: R 64 LEU cc_start: 0.8946 (tt) cc_final: 0.8613 (tm) REVERT: R 130 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7241 (mp0) REVERT: S 111 PHE cc_start: 0.8314 (m-80) cc_final: 0.8114 (m-80) REVERT: S 194 MET cc_start: 0.8599 (mtm) cc_final: 0.7894 (mtm) REVERT: S 342 ARG cc_start: 0.7537 (ptp-110) cc_final: 0.7322 (ptm160) REVERT: T 55 GLU cc_start: 0.7260 (pt0) cc_final: 0.7016 (pm20) REVERT: T 71 MET cc_start: 0.9257 (mtm) cc_final: 0.8929 (mtp) REVERT: T 283 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: T 342 ARG cc_start: 0.7357 (ptp-110) cc_final: 0.7135 (ptp-110) outliers start: 140 outliers final: 88 residues processed: 889 average time/residue: 1.7637 time to fit residues: 1917.2397 Evaluate side-chains 856 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 760 time to evaluate : 5.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 55 GLU 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 201 LEU 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 D residue 201 LEU 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 97 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 55 GLU 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 201 LEU 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 I residue 201 LEU 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 97 VAL Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 55 GLU 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 201 LEU 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 N residue 201 LEU 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 97 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 55 GLU 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 201 LEU 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 S residue 201 LEU 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 97 VAL Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 677 optimal weight: 0.0170 chunk 515 optimal weight: 3.9990 chunk 355 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 460 optimal weight: 0.0980 chunk 688 optimal weight: 3.9990 chunk 728 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 652 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN B 26 GLN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS C 26 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS D 26 GLN D 356 GLN E 89 HIS ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN G 26 GLN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 HIS H 26 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 HIS I 26 GLN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN J 89 HIS K 364 ASN L 26 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 HIS M 26 GLN ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 HIS N 26 GLN N 356 GLN O 45 ASN O 89 HIS P 364 ASN Q 26 GLN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 HIS R 26 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS S 26 GLN S 356 GLN T 89 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 63078 Z= 0.162 Angle : 0.489 7.417 85612 Z= 0.262 Chirality : 0.039 0.159 9820 Planarity : 0.004 0.057 10520 Dihedral : 11.033 73.854 10454 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.22 % Allowed : 13.09 % Favored : 84.70 % 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: 1.63 (0.10), residues: 7540 helix: 1.62 (0.07), residues: 4720 sheet: 0.72 (0.25), residues: 260 loop : 0.24 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 260 HIS 0.005 0.001 HIS B 225 PHE 0.008 0.002 PHE M 226 TYR 0.011 0.001 TYR P 337 ARG 0.011 0.001 ARG T 338 *********************** REFINEMENT MACRO_CYCLE 4 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 to be fit. rotamer outliers: 140 poor density : 840 time to evaluate : 5.132 Fit side-chains REVERT: A 67 MET cc_start: 0.8683 (mmm) cc_final: 0.8386 (mmm) REVERT: A 77 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 85 ASP cc_start: 0.7802 (m-30) cc_final: 0.7598 (m-30) REVERT: A 198 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (mmtt) REVERT: A 364 ASN cc_start: 0.7790 (t0) cc_final: 0.7567 (t0) REVERT: B 192 ASN cc_start: 0.8367 (m110) cc_final: 0.8109 (m-40) REVERT: B 271 MET cc_start: 0.8338 (mmm) cc_final: 0.7808 (mmm) REVERT: B 292 GLN cc_start: 0.8125 (pt0) cc_final: 0.7923 (mt0) REVERT: B 364 ASN cc_start: 0.8105 (t0) cc_final: 0.7735 (t0) REVERT: B 366 SER cc_start: 0.8351 (m) cc_final: 0.7922 (p) REVERT: C 64 LEU cc_start: 0.8924 (tt) cc_final: 0.8584 (tm) REVERT: C 130 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7227 (mp0) REVERT: D 342 ARG cc_start: 0.7537 (ptp-110) cc_final: 0.7333 (ptp-170) REVERT: E 71 MET cc_start: 0.9243 (mtm) cc_final: 0.8897 (mtp) REVERT: E 77 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7277 (mm-30) REVERT: E 342 ARG cc_start: 0.7429 (ptp-110) cc_final: 0.7209 (ptp-170) REVERT: F 67 MET cc_start: 0.8679 (mmm) cc_final: 0.8383 (mmm) REVERT: F 77 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7331 (mm-30) REVERT: F 85 ASP cc_start: 0.7800 (m-30) cc_final: 0.7596 (m-30) REVERT: F 198 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7908 (mmtt) REVERT: F 364 ASN cc_start: 0.7790 (t0) cc_final: 0.7567 (t0) REVERT: G 192 ASN cc_start: 0.8365 (m110) cc_final: 0.8098 (m-40) REVERT: G 271 MET cc_start: 0.8339 (mmm) cc_final: 0.7808 (mmm) REVERT: G 292 GLN cc_start: 0.8136 (pt0) cc_final: 0.7929 (mt0) REVERT: G 364 ASN cc_start: 0.8100 (t0) cc_final: 0.7728 (t0) REVERT: G 366 SER cc_start: 0.8351 (m) cc_final: 0.7921 (p) REVERT: H 64 LEU cc_start: 0.8928 (tt) cc_final: 0.8584 (tm) REVERT: H 130 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7230 (mp0) REVERT: I 342 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7332 (ptp-170) REVERT: J 71 MET cc_start: 0.9242 (mtm) cc_final: 0.8902 (mtp) REVERT: J 130 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7426 (mm-30) REVERT: J 338 ARG cc_start: 0.6938 (ptt-90) cc_final: 0.6727 (ptt-90) REVERT: J 342 ARG cc_start: 0.7430 (ptp-110) cc_final: 0.7209 (ptp-170) REVERT: K 67 MET cc_start: 0.8685 (mmm) cc_final: 0.8383 (mmm) REVERT: K 77 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7330 (mm-30) REVERT: K 85 ASP cc_start: 0.7797 (m-30) cc_final: 0.7594 (m-30) REVERT: K 198 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7910 (mmtt) REVERT: K 364 ASN cc_start: 0.7793 (t0) cc_final: 0.7572 (t0) REVERT: L 192 ASN cc_start: 0.8370 (m110) cc_final: 0.8114 (m-40) REVERT: L 271 MET cc_start: 0.8337 (mmm) cc_final: 0.7809 (mmm) REVERT: L 292 GLN cc_start: 0.8122 (pt0) cc_final: 0.7921 (mt0) REVERT: L 364 ASN cc_start: 0.8104 (t0) cc_final: 0.7732 (t0) REVERT: L 366 SER cc_start: 0.8353 (m) cc_final: 0.7924 (p) REVERT: M 64 LEU cc_start: 0.8928 (tt) cc_final: 0.8584 (tm) REVERT: M 130 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7230 (mp0) REVERT: N 342 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7330 (ptp-170) REVERT: O 71 MET cc_start: 0.9242 (mtm) cc_final: 0.8901 (mtp) REVERT: O 77 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7273 (mm-30) REVERT: O 342 ARG cc_start: 0.7430 (ptp-110) cc_final: 0.7210 (ptp-170) REVERT: P 67 MET cc_start: 0.8674 (mmm) cc_final: 0.8380 (mmm) REVERT: P 77 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7329 (mm-30) REVERT: P 85 ASP cc_start: 0.7801 (m-30) cc_final: 0.7592 (m-30) REVERT: P 198 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7906 (mmtt) REVERT: P 364 ASN cc_start: 0.7788 (t0) cc_final: 0.7563 (t0) REVERT: Q 192 ASN cc_start: 0.8365 (m110) cc_final: 0.8100 (m-40) REVERT: Q 271 MET cc_start: 0.8336 (mmm) cc_final: 0.7804 (mmm) REVERT: Q 364 ASN cc_start: 0.8101 (t0) cc_final: 0.7728 (t0) REVERT: Q 366 SER cc_start: 0.8355 (m) cc_final: 0.7922 (p) REVERT: R 64 LEU cc_start: 0.8930 (tt) cc_final: 0.8588 (tm) REVERT: R 130 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7228 (mp0) REVERT: S 342 ARG cc_start: 0.7536 (ptp-110) cc_final: 0.7332 (ptp-170) REVERT: T 71 MET cc_start: 0.9268 (mtm) cc_final: 0.8922 (mtp) REVERT: T 130 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7425 (mm-30) REVERT: T 342 ARG cc_start: 0.7427 (ptp-110) cc_final: 0.7207 (ptp-170) outliers start: 140 outliers final: 79 residues processed: 900 average time/residue: 1.7024 time to fit residues: 1887.7802 Evaluate side-chains 868 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 785 time to evaluate : 5.023 ------------------------------------------------------------------------------- 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 76 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 248 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 248 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL 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 76 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 248 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 248 MET Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP 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 76 ARG Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 248 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 248 MET Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 155 ASP 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 76 ARG Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 198 LYS Chi-restraints excluded: chain P residue 248 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 248 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 606 optimal weight: 4.9990 chunk 413 optimal weight: 0.0570 chunk 10 optimal weight: 0.2980 chunk 542 optimal weight: 4.9990 chunk 300 optimal weight: 0.0000 chunk 621 optimal weight: 3.9990 chunk 503 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 chunk 654 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 292 GLN E 364 ASN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 364 ASN J 292 GLN J 364 ASN ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN O 292 GLN O 364 ASN ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN T 292 GLN T 364 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 63078 Z= 0.242 Angle : 0.531 8.587 85612 Z= 0.282 Chirality : 0.041 0.169 9820 Planarity : 0.004 0.049 10520 Dihedral : 11.055 74.067 10454 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.56 % Allowed : 14.60 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.09), residues: 7540 helix: 1.43 (0.07), residues: 4720 sheet: 0.84 (0.25), residues: 260 loop : 0.20 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 260 HIS 0.006 0.001 HIS S 225 PHE 0.010 0.002 PHE B 223 TYR 0.013 0.001 TYR K 337 ARG 0.009 0.001 ARG E 338 *********************** REFINEMENT MACRO_CYCLE 5 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 946 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 784 time to evaluate : 5.182 Fit side-chains REVERT: A 67 MET cc_start: 0.8672 (mmm) cc_final: 0.8314 (mmm) REVERT: A 85 ASP cc_start: 0.7841 (m-30) cc_final: 0.7613 (m-30) REVERT: A 364 ASN cc_start: 0.7739 (t0) cc_final: 0.7477 (t0) REVERT: B 192 ASN cc_start: 0.8396 (m110) cc_final: 0.8121 (m-40) REVERT: B 271 MET cc_start: 0.8359 (mmm) cc_final: 0.7870 (mmm) REVERT: B 342 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6970 (mtt90) REVERT: B 366 SER cc_start: 0.8365 (m) cc_final: 0.8065 (p) REVERT: C 64 LEU cc_start: 0.8993 (tt) cc_final: 0.8675 (tm) REVERT: C 85 ASP cc_start: 0.7879 (m-30) cc_final: 0.7636 (m-30) REVERT: C 130 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7264 (mp0) REVERT: D 342 ARG cc_start: 0.7594 (ptp-110) cc_final: 0.7387 (ptp-170) REVERT: E 71 MET cc_start: 0.9238 (mtm) cc_final: 0.8866 (mtp) REVERT: E 77 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7251 (mm-30) REVERT: F 67 MET cc_start: 0.8669 (mmm) cc_final: 0.8311 (mmm) REVERT: F 85 ASP cc_start: 0.7837 (m-30) cc_final: 0.7607 (m-30) REVERT: F 364 ASN cc_start: 0.7738 (t0) cc_final: 0.7477 (t0) REVERT: G 192 ASN cc_start: 0.8396 (m110) cc_final: 0.8121 (m-40) REVERT: G 271 MET cc_start: 0.8356 (mmm) cc_final: 0.7863 (mmm) REVERT: G 342 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6971 (mtt90) REVERT: G 366 SER cc_start: 0.8363 (m) cc_final: 0.8058 (p) REVERT: H 64 LEU cc_start: 0.8995 (tt) cc_final: 0.8675 (tm) REVERT: H 85 ASP cc_start: 0.7881 (m-30) cc_final: 0.7636 (m-30) REVERT: H 130 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7271 (mp0) REVERT: I 342 ARG cc_start: 0.7593 (ptp-110) cc_final: 0.7387 (ptp-170) REVERT: J 71 MET cc_start: 0.9236 (mtm) cc_final: 0.8872 (mtp) REVERT: J 122 GLU cc_start: 0.7669 (mp0) cc_final: 0.7274 (mp0) REVERT: K 67 MET cc_start: 0.8673 (mmm) cc_final: 0.8312 (mmm) REVERT: K 85 ASP cc_start: 0.7837 (m-30) cc_final: 0.7607 (m-30) REVERT: K 364 ASN cc_start: 0.7740 (t0) cc_final: 0.7482 (t0) REVERT: L 192 ASN cc_start: 0.8401 (m110) cc_final: 0.8127 (m-40) REVERT: L 271 MET cc_start: 0.8359 (mmm) cc_final: 0.7869 (mmm) REVERT: L 342 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6968 (mtt90) REVERT: L 366 SER cc_start: 0.8369 (m) cc_final: 0.8065 (p) REVERT: M 64 LEU cc_start: 0.8995 (tt) cc_final: 0.8672 (tm) REVERT: M 85 ASP cc_start: 0.7878 (m-30) cc_final: 0.7636 (m-30) REVERT: M 130 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7268 (mp0) REVERT: N 342 ARG cc_start: 0.7588 (ptp-110) cc_final: 0.7385 (ptp-170) REVERT: O 71 MET cc_start: 0.9236 (mtm) cc_final: 0.8871 (mtp) REVERT: O 77 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7251 (mm-30) REVERT: P 67 MET cc_start: 0.8662 (mmm) cc_final: 0.8307 (mmm) REVERT: P 85 ASP cc_start: 0.7839 (m-30) cc_final: 0.7608 (m-30) REVERT: P 364 ASN cc_start: 0.7734 (t0) cc_final: 0.7472 (t0) REVERT: Q 50 MET cc_start: 0.8932 (mtm) cc_final: 0.8701 (mtm) REVERT: Q 192 ASN cc_start: 0.8396 (m110) cc_final: 0.8121 (m-40) REVERT: Q 271 MET cc_start: 0.8356 (mmm) cc_final: 0.7861 (mmm) REVERT: Q 342 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6974 (mtt90) REVERT: Q 366 SER cc_start: 0.8371 (m) cc_final: 0.8062 (p) REVERT: R 64 LEU cc_start: 0.8998 (tt) cc_final: 0.8679 (tm) REVERT: R 85 ASP cc_start: 0.7878 (m-30) cc_final: 0.7634 (m-30) REVERT: R 130 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7268 (mp0) REVERT: S 342 ARG cc_start: 0.7593 (ptp-110) cc_final: 0.7388 (ptp-170) REVERT: T 71 MET cc_start: 0.9234 (mtm) cc_final: 0.8869 (mtp) REVERT: T 122 GLU cc_start: 0.7673 (mp0) cc_final: 0.7276 (mp0) outliers start: 162 outliers final: 98 residues processed: 855 average time/residue: 1.7403 time to fit residues: 1832.8502 Evaluate side-chains 848 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 746 time to evaluate : 5.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 369 ASP 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 B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 201 LEU 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 D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 369 ASP 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 G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 201 LEU 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 I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 369 ASP 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 L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 201 LEU 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 N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 369 ASP 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 Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 201 LEU 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 S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 245 optimal weight: 0.7980 chunk 656 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 427 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 729 optimal weight: 0.6980 chunk 605 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 241 optimal weight: 0.9990 chunk 382 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1845 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= 0.213 Angle : 0.522 8.831 85612 Z= 0.277 Chirality : 0.041 0.158 9820 Planarity : 0.004 0.058 10520 Dihedral : 11.040 73.933 10454 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.28 % Allowed : 15.97 % Favored : 81.76 % 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: 1.46 (0.09), residues: 7540 helix: 1.46 (0.07), residues: 4720 sheet: 1.54 (0.25), residues: 220 loop : 0.14 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 260 HIS 0.005 0.001 HIS L 225 PHE 0.010 0.002 PHE B 223 TYR 0.013 0.001 TYR P 337 ARG 0.014 0.001 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 6 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 929 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 785 time to evaluate : 5.136 Fit side-chains REVERT: A 67 MET cc_start: 0.8672 (mmm) cc_final: 0.8292 (mmm) REVERT: A 77 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 364 ASN cc_start: 0.7762 (t0) cc_final: 0.7500 (t0) REVERT: B 175 ASP cc_start: 0.7841 (p0) cc_final: 0.7604 (p0) REVERT: B 192 ASN cc_start: 0.8336 (m110) cc_final: 0.8081 (m-40) REVERT: B 271 MET cc_start: 0.8330 (mmm) cc_final: 0.7805 (mmm) REVERT: B 342 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7028 (mtt90) REVERT: B 366 SER cc_start: 0.8349 (m) cc_final: 0.8043 (p) REVERT: C 64 LEU cc_start: 0.9003 (tt) cc_final: 0.8678 (tm) REVERT: C 130 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7248 (mp0) REVERT: D 194 MET cc_start: 0.8479 (mtm) cc_final: 0.7698 (mtm) REVERT: D 342 ARG cc_start: 0.7492 (ptp-110) cc_final: 0.7292 (ptp-170) REVERT: E 71 MET cc_start: 0.9227 (mtm) cc_final: 0.8860 (mtp) REVERT: E 77 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7228 (mm-30) REVERT: E 283 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7316 (mt0) REVERT: E 342 ARG cc_start: 0.7353 (ptp-110) cc_final: 0.7128 (ptp-170) REVERT: E 364 ASN cc_start: 0.7820 (t0) cc_final: 0.7581 (t0) REVERT: F 67 MET cc_start: 0.8671 (mmm) cc_final: 0.8294 (mmm) REVERT: F 77 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7311 (mm-30) REVERT: F 364 ASN cc_start: 0.7760 (t0) cc_final: 0.7500 (t0) REVERT: G 175 ASP cc_start: 0.7847 (p0) cc_final: 0.7604 (p0) REVERT: G 192 ASN cc_start: 0.8337 (m110) cc_final: 0.8077 (m-40) REVERT: G 271 MET cc_start: 0.8327 (mmm) cc_final: 0.7801 (mmm) REVERT: G 342 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7029 (mtt90) REVERT: G 366 SER cc_start: 0.8346 (m) cc_final: 0.8041 (p) REVERT: H 64 LEU cc_start: 0.9007 (tt) cc_final: 0.8679 (tm) REVERT: H 130 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7257 (mp0) REVERT: I 194 MET cc_start: 0.8481 (mtm) cc_final: 0.7701 (mtm) REVERT: J 71 MET cc_start: 0.9228 (mtm) cc_final: 0.8867 (mtp) REVERT: J 283 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: J 342 ARG cc_start: 0.7356 (ptp-110) cc_final: 0.7112 (ptm160) REVERT: J 364 ASN cc_start: 0.7812 (t0) cc_final: 0.7574 (t0) REVERT: K 67 MET cc_start: 0.8675 (mmm) cc_final: 0.8291 (mmm) REVERT: K 77 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7310 (mm-30) REVERT: K 198 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8078 (mmtt) REVERT: K 364 ASN cc_start: 0.7762 (t0) cc_final: 0.7503 (t0) REVERT: L 175 ASP cc_start: 0.7846 (p0) cc_final: 0.7605 (p0) REVERT: L 192 ASN cc_start: 0.8341 (m110) cc_final: 0.8085 (m-40) REVERT: L 271 MET cc_start: 0.8329 (mmm) cc_final: 0.7804 (mmm) REVERT: L 342 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7030 (mtt90) REVERT: L 366 SER cc_start: 0.8351 (m) cc_final: 0.8042 (p) REVERT: M 64 LEU cc_start: 0.9006 (tt) cc_final: 0.8677 (tm) REVERT: M 130 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7254 (mp0) REVERT: N 194 MET cc_start: 0.8480 (mtm) cc_final: 0.7699 (mtm) REVERT: O 71 MET cc_start: 0.9226 (mtm) cc_final: 0.8864 (mtp) REVERT: O 77 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7228 (mm-30) REVERT: O 283 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: O 342 ARG cc_start: 0.7352 (ptp-110) cc_final: 0.7128 (ptp-170) REVERT: O 364 ASN cc_start: 0.7813 (t0) cc_final: 0.7573 (t0) REVERT: P 67 MET cc_start: 0.8665 (mmm) cc_final: 0.8288 (mmm) REVERT: P 77 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7311 (mm-30) REVERT: P 364 ASN cc_start: 0.7755 (t0) cc_final: 0.7495 (t0) REVERT: Q 175 ASP cc_start: 0.7848 (p0) cc_final: 0.7606 (p0) REVERT: Q 192 ASN cc_start: 0.8337 (m110) cc_final: 0.8080 (m-40) REVERT: Q 271 MET cc_start: 0.8326 (mmm) cc_final: 0.7798 (mmm) REVERT: Q 342 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7032 (mtt90) REVERT: Q 366 SER cc_start: 0.8351 (m) cc_final: 0.8044 (p) REVERT: R 64 LEU cc_start: 0.9008 (tt) cc_final: 0.8682 (tm) REVERT: R 130 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7252 (mp0) REVERT: S 194 MET cc_start: 0.8480 (mtm) cc_final: 0.7700 (mtm) REVERT: T 71 MET cc_start: 0.9229 (mtm) cc_final: 0.8866 (mtp) REVERT: T 283 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7315 (mt0) REVERT: T 342 ARG cc_start: 0.7353 (ptp-110) cc_final: 0.7127 (ptp-170) REVERT: T 364 ASN cc_start: 0.7813 (t0) cc_final: 0.7574 (t0) outliers start: 144 outliers final: 102 residues processed: 854 average time/residue: 1.7069 time to fit residues: 1796.6820 Evaluate side-chains 864 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 753 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 9 ASN 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 B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 201 LEU 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 D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 9 ASN 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 G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 201 LEU 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 I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 9 ASN 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 L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 201 LEU 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 N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 9 ASN 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 Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 201 LEU 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 S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 703 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 415 optimal weight: 4.9990 chunk 532 optimal weight: 4.9990 chunk 412 optimal weight: 3.9990 chunk 614 optimal weight: 1.9990 chunk 407 optimal weight: 0.9980 chunk 726 optimal weight: 1.9990 chunk 454 optimal weight: 3.9990 chunk 443 optimal weight: 1.9990 chunk 335 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 89 HIS ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 ASN N 356 GLN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 63078 Z= 0.342 Angle : 0.593 9.816 85612 Z= 0.313 Chirality : 0.044 0.212 9820 Planarity : 0.005 0.067 10520 Dihedral : 11.149 74.321 10454 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.37 % Allowed : 16.23 % Favored : 81.39 % 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: 1.13 (0.09), residues: 7540 helix: 1.15 (0.07), residues: 4720 sheet: 1.75 (0.26), residues: 220 loop : 0.07 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 260 HIS 0.009 0.002 HIS L 225 PHE 0.012 0.002 PHE P 243 TYR 0.017 0.002 TYR K 337 ARG 0.012 0.001 ARG E 342 *********************** REFINEMENT MACRO_CYCLE 7 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 902 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 752 time to evaluate : 5.993 Fit side-chains REVERT: A 67 MET cc_start: 0.8689 (mmm) cc_final: 0.8451 (mmm) REVERT: A 193 GLU cc_start: 0.7616 (mp0) cc_final: 0.7335 (mp0) REVERT: A 364 ASN cc_start: 0.7858 (t0) cc_final: 0.7546 (t0) REVERT: B 175 ASP cc_start: 0.7896 (p0) cc_final: 0.7632 (p0) REVERT: B 271 MET cc_start: 0.8345 (mmm) cc_final: 0.7874 (mmm) REVERT: B 342 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7164 (mtt90) REVERT: B 366 SER cc_start: 0.8378 (m) cc_final: 0.8083 (p) REVERT: C 64 LEU cc_start: 0.9044 (tt) cc_final: 0.8762 (tm) REVERT: C 130 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7287 (mp0) REVERT: E 71 MET cc_start: 0.9224 (mtm) cc_final: 0.8849 (mtp) REVERT: E 77 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7207 (mm-30) REVERT: E 342 ARG cc_start: 0.7288 (ptp-110) cc_final: 0.7047 (ptp-110) REVERT: F 67 MET cc_start: 0.8683 (mmm) cc_final: 0.8448 (mmm) REVERT: F 193 GLU cc_start: 0.7618 (mp0) cc_final: 0.7335 (mp0) REVERT: F 364 ASN cc_start: 0.7857 (t0) cc_final: 0.7545 (t0) REVERT: G 175 ASP cc_start: 0.7904 (p0) cc_final: 0.7634 (p0) REVERT: G 271 MET cc_start: 0.8341 (mmm) cc_final: 0.7870 (mmm) REVERT: G 342 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7169 (mtt90) REVERT: G 366 SER cc_start: 0.8374 (m) cc_final: 0.8079 (p) REVERT: H 64 LEU cc_start: 0.9048 (tt) cc_final: 0.8763 (tm) REVERT: H 130 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7296 (mp0) REVERT: I 342 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7191 (mtt180) REVERT: J 71 MET cc_start: 0.9229 (mtm) cc_final: 0.8864 (mtp) REVERT: J 342 ARG cc_start: 0.7289 (ptp-110) cc_final: 0.7050 (ptp-110) REVERT: K 67 MET cc_start: 0.8685 (mmm) cc_final: 0.8445 (mmm) REVERT: K 193 GLU cc_start: 0.7603 (mp0) cc_final: 0.7320 (mp0) REVERT: K 364 ASN cc_start: 0.7858 (t0) cc_final: 0.7549 (t0) REVERT: L 175 ASP cc_start: 0.7903 (p0) cc_final: 0.7635 (p0) REVERT: L 271 MET cc_start: 0.8344 (mmm) cc_final: 0.7873 (mmm) REVERT: L 342 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7168 (mtt90) REVERT: L 366 SER cc_start: 0.8381 (m) cc_final: 0.8082 (p) REVERT: M 64 LEU cc_start: 0.9048 (tt) cc_final: 0.8760 (tm) REVERT: M 130 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7296 (mp0) REVERT: N 342 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7188 (mtt180) REVERT: O 71 MET cc_start: 0.9222 (mtm) cc_final: 0.8853 (mtp) REVERT: O 77 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7204 (mm-30) REVERT: O 342 ARG cc_start: 0.7287 (ptp-110) cc_final: 0.7048 (ptp-110) REVERT: P 67 MET cc_start: 0.8680 (mmm) cc_final: 0.8443 (mmm) REVERT: P 193 GLU cc_start: 0.7622 (mp0) cc_final: 0.7337 (mp0) REVERT: P 364 ASN cc_start: 0.7853 (t0) cc_final: 0.7542 (t0) REVERT: Q 50 MET cc_start: 0.9018 (mtm) cc_final: 0.8751 (mtm) REVERT: Q 271 MET cc_start: 0.8340 (mmm) cc_final: 0.7862 (mmm) REVERT: Q 342 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7167 (mtt90) REVERT: Q 366 SER cc_start: 0.8381 (m) cc_final: 0.8083 (p) REVERT: R 64 LEU cc_start: 0.9049 (tt) cc_final: 0.8765 (tm) REVERT: R 130 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7293 (mp0) REVERT: S 342 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7187 (mtt180) REVERT: T 71 MET cc_start: 0.9228 (mtm) cc_final: 0.8862 (mtp) REVERT: T 342 ARG cc_start: 0.7286 (ptp-110) cc_final: 0.7048 (ptp-110) outliers start: 150 outliers final: 94 residues processed: 811 average time/residue: 1.7835 time to fit residues: 1774.3026 Evaluate side-chains 840 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 739 time to evaluate : 5.303 ------------------------------------------------------------------------------- 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 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 76 ARG 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 D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 239 VAL 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 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 76 ARG 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 I residue 201 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL 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 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 76 ARG 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 N residue 201 LEU Chi-restraints excluded: chain N residue 342 ARG Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 239 VAL 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 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 76 ARG 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 S residue 201 LEU Chi-restraints excluded: chain S residue 342 ARG Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 449 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 434 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 462 optimal weight: 1.9990 chunk 495 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 571 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS C 45 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 ASN ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1893 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= 0.207 Angle : 0.528 10.646 85612 Z= 0.280 Chirality : 0.040 0.155 9820 Planarity : 0.004 0.064 10520 Dihedral : 11.072 73.919 10454 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.98 % Allowed : 16.60 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.09), residues: 7540 helix: 1.38 (0.07), residues: 4720 sheet: 1.57 (0.25), residues: 220 loop : 0.11 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 260 HIS 0.005 0.001 HIS B 225 PHE 0.010 0.002 PHE L 223 TYR 0.012 0.001 TYR K 337 ARG 0.013 0.001 ARG J 338 *********************** REFINEMENT MACRO_CYCLE 8 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 877 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 752 time to evaluate : 5.122 Fit side-chains REVERT: A 67 MET cc_start: 0.8666 (mmm) cc_final: 0.8316 (mmm) REVERT: A 77 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 364 ASN cc_start: 0.7829 (t0) cc_final: 0.7550 (t0) REVERT: B 271 MET cc_start: 0.8326 (mmm) cc_final: 0.7815 (mmm) REVERT: B 342 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7147 (mtt90) REVERT: B 366 SER cc_start: 0.8328 (m) cc_final: 0.8025 (p) REVERT: C 64 LEU cc_start: 0.9004 (tt) cc_final: 0.8683 (tm) REVERT: C 130 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7254 (mp0) REVERT: C 342 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: D 194 MET cc_start: 0.8459 (mtm) cc_final: 0.7737 (mtm) REVERT: D 342 ARG cc_start: 0.7612 (ptp-170) cc_final: 0.7235 (mtt180) REVERT: E 71 MET cc_start: 0.9244 (mtm) cc_final: 0.8899 (mtp) REVERT: E 77 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7210 (mm-30) REVERT: F 67 MET cc_start: 0.8661 (mmm) cc_final: 0.8313 (mmm) REVERT: F 77 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7283 (mm-30) REVERT: F 364 ASN cc_start: 0.7827 (t0) cc_final: 0.7550 (t0) REVERT: G 271 MET cc_start: 0.8322 (mmm) cc_final: 0.7807 (mmm) REVERT: G 292 GLN cc_start: 0.8164 (pt0) cc_final: 0.7866 (mt0) REVERT: G 342 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7133 (mtt90) REVERT: G 366 SER cc_start: 0.8324 (m) cc_final: 0.8018 (p) REVERT: H 64 LEU cc_start: 0.9005 (tt) cc_final: 0.8682 (tm) REVERT: H 130 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7263 (mp0) REVERT: H 342 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7314 (mtt180) REVERT: I 194 MET cc_start: 0.8460 (mtm) cc_final: 0.7743 (mtm) REVERT: I 342 ARG cc_start: 0.7546 (ptp-170) cc_final: 0.7241 (mtt180) REVERT: J 71 MET cc_start: 0.9242 (mtm) cc_final: 0.8903 (mtp) REVERT: K 67 MET cc_start: 0.8666 (mmm) cc_final: 0.8313 (mmm) REVERT: K 77 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7282 (mm-30) REVERT: K 364 ASN cc_start: 0.7829 (t0) cc_final: 0.7556 (t0) REVERT: L 271 MET cc_start: 0.8326 (mmm) cc_final: 0.7810 (mmm) REVERT: L 292 GLN cc_start: 0.8149 (pt0) cc_final: 0.7854 (mt0) REVERT: L 342 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7150 (mtt90) REVERT: L 366 SER cc_start: 0.8327 (m) cc_final: 0.8020 (p) REVERT: M 64 LEU cc_start: 0.9007 (tt) cc_final: 0.8681 (tm) REVERT: M 130 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7258 (mp0) REVERT: M 342 ARG cc_start: 0.7696 (ptp-110) cc_final: 0.7313 (mtt180) REVERT: N 194 MET cc_start: 0.8459 (mtm) cc_final: 0.7740 (mtm) REVERT: N 342 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.7234 (mtt180) REVERT: O 71 MET cc_start: 0.9242 (mtm) cc_final: 0.8903 (mtp) REVERT: O 77 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7209 (mm-30) REVERT: P 67 MET cc_start: 0.8658 (mmm) cc_final: 0.8309 (mmm) REVERT: P 77 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7285 (mm-30) REVERT: P 364 ASN cc_start: 0.7824 (t0) cc_final: 0.7547 (t0) REVERT: Q 50 MET cc_start: 0.8939 (mtm) cc_final: 0.8709 (mtm) REVERT: Q 271 MET cc_start: 0.8321 (mmm) cc_final: 0.7808 (mmm) REVERT: Q 342 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7152 (mtt90) REVERT: Q 366 SER cc_start: 0.8332 (m) cc_final: 0.8023 (p) REVERT: R 64 LEU cc_start: 0.9007 (tt) cc_final: 0.8684 (tm) REVERT: R 130 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7259 (mp0) REVERT: R 342 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7315 (mtt180) REVERT: S 194 MET cc_start: 0.8461 (mtm) cc_final: 0.7741 (mtm) REVERT: S 342 ARG cc_start: 0.7543 (ptp-170) cc_final: 0.7236 (mtt180) REVERT: T 71 MET cc_start: 0.9242 (mtm) cc_final: 0.8904 (mtp) outliers start: 125 outliers final: 103 residues processed: 810 average time/residue: 1.7695 time to fit residues: 1758.5312 Evaluate side-chains 852 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 742 time to evaluate : 5.103 ------------------------------------------------------------------------------- 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 A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 9 ASN 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 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL 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 F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 9 ASN 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 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 342 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 239 VAL 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 K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 9 ASN 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 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 76 ARG 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 N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL 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 P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 9 ASN 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 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain R residue 342 ARG Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 661 optimal weight: 0.7980 chunk 696 optimal weight: 0.9980 chunk 635 optimal weight: 0.9990 chunk 677 optimal weight: 2.9990 chunk 407 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 531 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 611 optimal weight: 0.9990 chunk 640 optimal weight: 0.0000 chunk 674 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 364 ASN ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 63078 Z= 0.179 Angle : 0.516 10.775 85612 Z= 0.272 Chirality : 0.039 0.157 9820 Planarity : 0.004 0.061 10520 Dihedral : 11.047 73.880 10454 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.06 % Allowed : 16.63 % Favored : 81.31 % 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: 1.54 (0.10), residues: 7540 helix: 1.53 (0.07), residues: 4720 sheet: 1.71 (0.25), residues: 220 loop : 0.15 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 260 HIS 0.005 0.001 HIS L 225 PHE 0.010 0.002 PHE G 223 TYR 0.012 0.001 TYR A 337 ARG 0.015 0.001 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 9 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 873 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 743 time to evaluate : 5.160 Fit side-chains REVERT: A 67 MET cc_start: 0.8691 (mmm) cc_final: 0.8389 (mmm) REVERT: A 77 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7317 (mm-30) REVERT: A 364 ASN cc_start: 0.7799 (t0) cc_final: 0.7527 (t0) REVERT: B 271 MET cc_start: 0.8317 (mmm) cc_final: 0.7785 (mmm) REVERT: B 292 GLN cc_start: 0.8121 (pt0) cc_final: 0.7828 (mt0) REVERT: B 342 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7144 (mtt90) REVERT: B 366 SER cc_start: 0.8322 (m) cc_final: 0.8008 (p) REVERT: C 64 LEU cc_start: 0.8986 (tt) cc_final: 0.8648 (tm) REVERT: C 89 HIS cc_start: 0.7014 (m-70) cc_final: 0.6656 (m170) REVERT: C 130 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7209 (mp0) REVERT: D 342 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.7186 (mtt180) REVERT: E 71 MET cc_start: 0.9238 (mtm) cc_final: 0.8901 (mtp) REVERT: E 77 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7233 (mm-30) REVERT: F 67 MET cc_start: 0.8690 (mmm) cc_final: 0.8388 (mmm) REVERT: F 77 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7317 (mm-30) REVERT: F 364 ASN cc_start: 0.7799 (t0) cc_final: 0.7528 (t0) REVERT: G 271 MET cc_start: 0.8318 (mmm) cc_final: 0.7787 (mmm) REVERT: G 292 GLN cc_start: 0.8132 (pt0) cc_final: 0.7836 (mt0) REVERT: G 342 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7150 (mtt90) REVERT: G 366 SER cc_start: 0.8319 (m) cc_final: 0.8002 (p) REVERT: H 64 LEU cc_start: 0.8988 (tt) cc_final: 0.8648 (tm) REVERT: H 89 HIS cc_start: 0.7067 (m-70) cc_final: 0.6710 (m170) REVERT: H 130 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7213 (mp0) REVERT: I 342 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7263 (mtt180) REVERT: J 71 MET cc_start: 0.9214 (mtm) cc_final: 0.8871 (mtp) REVERT: K 67 MET cc_start: 0.8693 (mmm) cc_final: 0.8384 (mmm) REVERT: K 77 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7319 (mm-30) REVERT: K 364 ASN cc_start: 0.7798 (t0) cc_final: 0.7529 (t0) REVERT: L 271 MET cc_start: 0.8318 (mmm) cc_final: 0.7786 (mmm) REVERT: L 292 GLN cc_start: 0.8119 (pt0) cc_final: 0.7827 (mt0) REVERT: L 342 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7148 (mtt90) REVERT: L 366 SER cc_start: 0.8321 (m) cc_final: 0.8003 (p) REVERT: M 64 LEU cc_start: 0.8988 (tt) cc_final: 0.8647 (tm) REVERT: M 89 HIS cc_start: 0.7003 (m-70) cc_final: 0.6654 (m170) REVERT: M 130 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7214 (mp0) REVERT: M 342 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7294 (mtt180) REVERT: N 342 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7259 (mtt180) REVERT: O 71 MET cc_start: 0.9237 (mtm) cc_final: 0.8907 (mtp) REVERT: O 77 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7229 (mm-30) REVERT: P 67 MET cc_start: 0.8684 (mmm) cc_final: 0.8384 (mmm) REVERT: P 77 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7319 (mm-30) REVERT: P 364 ASN cc_start: 0.7799 (t0) cc_final: 0.7524 (t0) REVERT: Q 50 MET cc_start: 0.8938 (mtm) cc_final: 0.8720 (mtm) REVERT: Q 271 MET cc_start: 0.8314 (mmm) cc_final: 0.7782 (mmm) REVERT: Q 342 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7150 (mtt90) REVERT: Q 366 SER cc_start: 0.8326 (m) cc_final: 0.8009 (p) REVERT: R 64 LEU cc_start: 0.8991 (tt) cc_final: 0.8651 (tm) REVERT: R 89 HIS cc_start: 0.7011 (m-70) cc_final: 0.6656 (m170) REVERT: R 130 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7211 (mp0) REVERT: S 342 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7262 (mtt180) REVERT: T 71 MET cc_start: 0.9215 (mtm) cc_final: 0.8871 (mtp) outliers start: 130 outliers final: 93 residues processed: 808 average time/residue: 1.7898 time to fit residues: 1779.9763 Evaluate side-chains 832 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 731 time to evaluate : 5.089 ------------------------------------------------------------------------------- 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 A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP 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 D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL 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 F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG 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 I residue 201 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP 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 K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 342 ARG Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL 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 P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG 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 S residue 201 LEU Chi-restraints excluded: chain S residue 342 ARG Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 444 optimal weight: 3.9990 chunk 716 optimal weight: 0.1980 chunk 437 optimal weight: 0.8980 chunk 339 optimal weight: 0.8980 chunk 497 optimal weight: 0.9980 chunk 751 optimal weight: 3.9990 chunk 691 optimal weight: 0.5980 chunk 598 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 462 optimal weight: 0.5980 chunk 366 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 63078 Z= 0.157 Angle : 0.508 10.875 85612 Z= 0.267 Chirality : 0.039 0.160 9820 Planarity : 0.004 0.055 10520 Dihedral : 11.005 73.835 10454 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.60 % Allowed : 16.95 % Favored : 81.46 % 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: 1.67 (0.10), residues: 7540 helix: 1.65 (0.07), residues: 4720 sheet: 1.66 (0.25), residues: 220 loop : 0.18 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 260 HIS 0.004 0.001 HIS L 225 PHE 0.009 0.001 PHE C 226 TYR 0.011 0.001 TYR P 337 ARG 0.013 0.001 ARG E 338 ********************** REFINEMENT MACRO_CYCLE 10 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 851 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 750 time to evaluate : 5.151 Fit side-chains REVERT: A 67 MET cc_start: 0.8639 (mmm) cc_final: 0.8407 (mmm) REVERT: A 77 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7290 (mm-30) REVERT: A 364 ASN cc_start: 0.7912 (t0) cc_final: 0.7635 (t0) REVERT: B 271 MET cc_start: 0.8314 (mmm) cc_final: 0.7778 (mmm) REVERT: B 292 GLN cc_start: 0.8094 (pt0) cc_final: 0.7874 (mt0) REVERT: B 342 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7129 (mtt90) REVERT: B 364 ASN cc_start: 0.8112 (t0) cc_final: 0.7714 (t0) REVERT: B 366 SER cc_start: 0.8314 (m) cc_final: 0.7861 (p) REVERT: C 89 HIS cc_start: 0.6996 (m-70) cc_final: 0.6684 (m170) REVERT: C 130 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7265 (mp0) REVERT: C 364 ASN cc_start: 0.7888 (t0) cc_final: 0.7614 (t0) REVERT: D 122 GLU cc_start: 0.7606 (mp0) cc_final: 0.7403 (mp0) REVERT: D 342 ARG cc_start: 0.7584 (ptp-170) cc_final: 0.7169 (mtt180) REVERT: E 71 MET cc_start: 0.9207 (mtm) cc_final: 0.8855 (mtp) REVERT: E 77 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7228 (mm-30) REVERT: E 283 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7146 (mt0) REVERT: E 342 ARG cc_start: 0.7440 (ptm160) cc_final: 0.7207 (ptp-110) REVERT: F 67 MET cc_start: 0.8637 (mmm) cc_final: 0.8402 (mmm) REVERT: F 77 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7292 (mm-30) REVERT: F 364 ASN cc_start: 0.7911 (t0) cc_final: 0.7633 (t0) REVERT: G 271 MET cc_start: 0.8317 (mmm) cc_final: 0.7776 (mmm) REVERT: G 292 GLN cc_start: 0.8105 (pt0) cc_final: 0.7883 (mt0) REVERT: G 342 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7132 (mtt90) REVERT: G 364 ASN cc_start: 0.8070 (t0) cc_final: 0.7673 (t0) REVERT: G 366 SER cc_start: 0.8312 (m) cc_final: 0.7859 (p) REVERT: H 89 HIS cc_start: 0.7111 (m-70) cc_final: 0.6772 (m170) REVERT: H 130 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7272 (mp0) REVERT: H 364 ASN cc_start: 0.7887 (t0) cc_final: 0.7617 (t0) REVERT: I 122 GLU cc_start: 0.7606 (mp0) cc_final: 0.7405 (mp0) REVERT: I 342 ARG cc_start: 0.7549 (ptp-170) cc_final: 0.7255 (mtt180) REVERT: J 71 MET cc_start: 0.9204 (mtm) cc_final: 0.8858 (mtp) REVERT: J 342 ARG cc_start: 0.7439 (ptm160) cc_final: 0.7213 (ptp-110) REVERT: K 67 MET cc_start: 0.8642 (mmm) cc_final: 0.8406 (mmm) REVERT: K 77 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7288 (mm-30) REVERT: K 364 ASN cc_start: 0.7910 (t0) cc_final: 0.7635 (t0) REVERT: L 271 MET cc_start: 0.8314 (mmm) cc_final: 0.7779 (mmm) REVERT: L 292 GLN cc_start: 0.8093 (pt0) cc_final: 0.7874 (mt0) REVERT: L 342 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7131 (mtt90) REVERT: L 364 ASN cc_start: 0.8072 (t0) cc_final: 0.7676 (t0) REVERT: L 366 SER cc_start: 0.8312 (m) cc_final: 0.7858 (p) REVERT: M 89 HIS cc_start: 0.6998 (m-70) cc_final: 0.6685 (m170) REVERT: M 130 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7269 (mp0) REVERT: M 364 ASN cc_start: 0.7877 (t0) cc_final: 0.7605 (t0) REVERT: N 342 ARG cc_start: 0.7546 (ptp-170) cc_final: 0.7250 (mtt180) REVERT: O 71 MET cc_start: 0.9202 (mtm) cc_final: 0.8858 (mtp) REVERT: O 77 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7227 (mm-30) REVERT: O 283 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: O 342 ARG cc_start: 0.7438 (ptm160) cc_final: 0.7203 (ptp-110) REVERT: P 67 MET cc_start: 0.8678 (mmm) cc_final: 0.8444 (mmm) REVERT: P 77 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7290 (mm-30) REVERT: P 364 ASN cc_start: 0.7912 (t0) cc_final: 0.7634 (t0) REVERT: Q 271 MET cc_start: 0.8312 (mmm) cc_final: 0.7774 (mmm) REVERT: Q 342 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7134 (mtt90) REVERT: Q 364 ASN cc_start: 0.8070 (t0) cc_final: 0.7674 (t0) REVERT: Q 366 SER cc_start: 0.8318 (m) cc_final: 0.7864 (p) REVERT: R 89 HIS cc_start: 0.7003 (m-70) cc_final: 0.6685 (m170) REVERT: R 130 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7270 (mp0) REVERT: R 364 ASN cc_start: 0.7879 (t0) cc_final: 0.7607 (t0) REVERT: S 342 ARG cc_start: 0.7549 (ptp-170) cc_final: 0.7254 (mtt180) REVERT: T 71 MET cc_start: 0.9205 (mtm) cc_final: 0.8858 (mtp) REVERT: T 283 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7144 (mt0) REVERT: T 342 ARG cc_start: 0.7434 (ptm160) cc_final: 0.7203 (ptp-110) outliers start: 101 outliers final: 85 residues processed: 807 average time/residue: 1.8167 time to fit residues: 1799.8027 Evaluate side-chains 838 residues out of total 6280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 746 time to evaluate : 5.073 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP 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 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN 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 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP 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 I residue 155 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP 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 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP 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 N residue 155 ASP Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN 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 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP 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 S residue 155 ASP Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 475 optimal weight: 3.9990 chunk 637 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 551 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 166 optimal weight: 0.1980 chunk 599 optimal weight: 0.6980 chunk 250 optimal weight: 0.3980 chunk 615 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113999 restraints weight = 130881.956| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.80 r_work: 0.2897 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 63078 Z= 0.161 Angle : 0.512 11.791 85612 Z= 0.267 Chirality : 0.039 0.162 9820 Planarity : 0.004 0.060 10520 Dihedral : 10.984 73.862 10454 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.66 % Allowed : 17.04 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 7540 helix: 1.68 (0.07), residues: 4720 sheet: 1.80 (0.25), residues: 220 loop : 0.21 (0.13), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 260 HIS 0.004 0.001 HIS L 225 PHE 0.009 0.001 PHE H 226 TYR 0.010 0.001 TYR A 337 ARG 0.015 0.001 ARG R 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24012.33 seconds wall clock time: 415 minutes 17.71 seconds (24917.71 seconds total)