Starting phenix.real_space_refine on Sun Oct 13 22:43:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qje_18445/10_2024/8qje_18445.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qje_18445/10_2024/8qje_18445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qje_18445/10_2024/8qje_18445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qje_18445/10_2024/8qje_18445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qje_18445/10_2024/8qje_18445.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qje_18445/10_2024/8qje_18445.cif" } resolution = 4.16 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= 0.000 sd= 0.006 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 Zn 12 6.06 5 S 276 5.16 5 C 42996 2.51 5 N 11616 2.21 5 O 12780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 67680 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3554 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 13, 'TRANS': 425} Chain breaks: 1 Chain: "C" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, F, H, J, L, N, P, R, T, V, E, G, I, K, M, O, Q, S, U, W, X Time building chain proxies: 12.84, per 1000 atoms: 0.19 Number of scatterers: 67680 At special positions: 0 Unit cell: (169.56, 169.56, 220.32, 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) Zn 12 29.99 S 276 16.00 O 12780 8.00 N 11616 7.00 C 42996 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: 12.29 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" NE2 HIS C 117 " pdb=" ZN E 400 " pdb="ZN ZN E 400 " - pdb=" NE2 HIS E 117 " pdb=" ZN G 400 " pdb="ZN ZN G 400 " - pdb=" NE2 HIS G 117 " pdb=" ZN I 400 " pdb="ZN ZN I 400 " - pdb=" NE2 HIS I 117 " pdb=" ZN K 400 " pdb="ZN ZN K 400 " - pdb=" NE2 HIS K 117 " pdb=" ZN M 400 " pdb="ZN ZN M 400 " - pdb=" NE2 HIS M 117 " pdb=" ZN O 400 " pdb="ZN ZN O 400 " - pdb=" NE2 HIS O 117 " pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" NE2 HIS Q 117 " pdb=" ZN S 400 " pdb="ZN ZN S 400 " - pdb=" NE2 HIS S 117 " pdb=" ZN U 400 " pdb="ZN ZN U 400 " - pdb=" NE2 HIS U 117 " pdb=" ZN W 400 " pdb="ZN ZN W 400 " - pdb=" NE2 HIS W 117 " pdb=" ZN X 400 " pdb="ZN ZN X 400 " - pdb=" NE2 HIS X 117 " 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15552 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 84 sheets defined 44.6% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 153 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 317 Processing helix chain 'A' and resid 347 through 363 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 Processing helix chain 'A' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN W 39 " --> pdb=" O SER W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 46 Processing helix chain 'W' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL W 52 " --> pdb=" O SER W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR W 75 " --> pdb=" O GLY W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 112 Processing helix chain 'W' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU W 224 " --> pdb=" O PRO W 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU W 234 " --> pdb=" O TYR W 230 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 243 No H-bonds generated for 'chain 'W' and resid 241 through 243' Processing helix chain 'W' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP W 289 " --> pdb=" O LYS W 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA W 293 " --> pdb=" O ASP W 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR W 294 " --> pdb=" O GLY W 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE W 295 " --> pdb=" O LEU W 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 153 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.576A pdb=" N ARG B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 Processing helix chain 'B' and resid 347 through 363 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'B' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 495 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.693A pdb=" N VAL C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.667A pdb=" N LYS D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR D 111 " --> pdb=" O GLN D 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 153 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.576A pdb=" N ARG D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE D 281 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 317 Processing helix chain 'D' and resid 347 through 363 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 403 through 419 Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN D 450 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE D 451 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 Processing helix chain 'D' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 495 " --> pdb=" O TYR D 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN D 496 " --> pdb=" O ASN D 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS D 497 " --> pdb=" O ASP D 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU D 498 " --> pdb=" O GLY D 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU E 224 " --> pdb=" O PRO E 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 293 " --> pdb=" O ASP E 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS F 90 " --> pdb=" O ASP F 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR F 111 " --> pdb=" O GLN F 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 153 Processing helix chain 'F' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE F 282 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 317 Processing helix chain 'F' and resid 347 through 363 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 403 through 419 Processing helix chain 'F' and resid 420 through 422 No H-bonds generated for 'chain 'F' and resid 420 through 422' Processing helix chain 'F' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN F 450 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE F 451 " --> pdb=" O LEU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 462 Processing helix chain 'F' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN F 480 " --> pdb=" O ALA F 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 495 " --> pdb=" O TYR F 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN F 496 " --> pdb=" O ASN F 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS F 497 " --> pdb=" O ASP F 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 498 " --> pdb=" O GLY F 494 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 243 No H-bonds generated for 'chain 'G' and resid 241 through 243' Processing helix chain 'G' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 293 " --> pdb=" O ASP G 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS H 90 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE H 91 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET H 110 " --> pdb=" O ASN H 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR H 111 " --> pdb=" O GLN H 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 153 Processing helix chain 'H' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE H 263 " --> pdb=" O SER H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE H 281 " --> pdb=" O PHE H 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE H 282 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'H' and resid 347 through 363 Processing helix chain 'H' and resid 365 through 370 Processing helix chain 'H' and resid 396 through 403 Processing helix chain 'H' and resid 403 through 419 Processing helix chain 'H' and resid 420 through 422 No H-bonds generated for 'chain 'H' and resid 420 through 422' Processing helix chain 'H' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN H 450 " --> pdb=" O LYS H 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE H 451 " --> pdb=" O LEU H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 462 Processing helix chain 'H' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN H 480 " --> pdb=" O ALA H 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS H 495 " --> pdb=" O TYR H 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN H 496 " --> pdb=" O ASN H 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS H 497 " --> pdb=" O ASP H 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU H 498 " --> pdb=" O GLY H 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.693A pdb=" N VAL I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU I 224 " --> pdb=" O PRO I 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU I 234 " --> pdb=" O TYR I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 243 No H-bonds generated for 'chain 'I' and resid 241 through 243' Processing helix chain 'I' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU I 286 " --> pdb=" O GLU I 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP I 289 " --> pdb=" O LYS I 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR I 294 " --> pdb=" O GLY I 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE I 295 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 92 removed outlier: 3.667A pdb=" N LYS J 90 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET J 110 " --> pdb=" O ASN J 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR J 111 " --> pdb=" O GLN J 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS J 112 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 153 Processing helix chain 'J' and resid 163 through 178 removed outlier: 3.576A pdb=" N ARG J 173 " --> pdb=" O LYS J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE J 281 " --> pdb=" O PHE J 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE J 282 " --> pdb=" O ASN J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 317 Processing helix chain 'J' and resid 347 through 363 Processing helix chain 'J' and resid 365 through 370 Processing helix chain 'J' and resid 396 through 403 Processing helix chain 'J' and resid 403 through 419 Processing helix chain 'J' and resid 420 through 422 No H-bonds generated for 'chain 'J' and resid 420 through 422' Processing helix chain 'J' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE J 451 " --> pdb=" O LEU J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 462 Processing helix chain 'J' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN J 480 " --> pdb=" O ALA J 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS J 495 " --> pdb=" O TYR J 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN J 496 " --> pdb=" O ASN J 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS J 497 " --> pdb=" O ASP J 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU J 498 " --> pdb=" O GLY J 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR K 75 " --> pdb=" O GLY K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU K 224 " --> pdb=" O PRO K 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU K 234 " --> pdb=" O TYR K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 243 No H-bonds generated for 'chain 'K' and resid 241 through 243' Processing helix chain 'K' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR K 294 " --> pdb=" O GLY K 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS L 90 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE L 91 " --> pdb=" O VAL L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET L 110 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR L 111 " --> pdb=" O GLN L 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS L 112 " --> pdb=" O VAL L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 153 Processing helix chain 'L' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG L 173 " --> pdb=" O LYS L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE L 281 " --> pdb=" O PHE L 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE L 282 " --> pdb=" O ASN L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 317 Processing helix chain 'L' and resid 347 through 363 Processing helix chain 'L' and resid 365 through 370 Processing helix chain 'L' and resid 396 through 403 Processing helix chain 'L' and resid 403 through 419 Processing helix chain 'L' and resid 420 through 422 No H-bonds generated for 'chain 'L' and resid 420 through 422' Processing helix chain 'L' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN L 450 " --> pdb=" O LYS L 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE L 451 " --> pdb=" O LEU L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 462 Processing helix chain 'L' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN L 480 " --> pdb=" O ALA L 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS L 495 " --> pdb=" O TYR L 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN L 496 " --> pdb=" O ASN L 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS L 497 " --> pdb=" O ASP L 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU L 498 " --> pdb=" O GLY L 494 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 46 Processing helix chain 'M' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR M 75 " --> pdb=" O GLY M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'M' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU M 224 " --> pdb=" O PRO M 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU M 234 " --> pdb=" O TYR M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 243 No H-bonds generated for 'chain 'M' and resid 241 through 243' Processing helix chain 'M' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU M 286 " --> pdb=" O GLU M 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP M 289 " --> pdb=" O LYS M 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA M 293 " --> pdb=" O ASP M 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR M 294 " --> pdb=" O GLY M 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE M 295 " --> pdb=" O LEU M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS N 90 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE N 91 " --> pdb=" O VAL N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET N 110 " --> pdb=" O ASN N 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR N 111 " --> pdb=" O GLN N 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS N 112 " --> pdb=" O VAL N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 153 Processing helix chain 'N' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG N 173 " --> pdb=" O LYS N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE N 281 " --> pdb=" O PHE N 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE N 282 " --> pdb=" O ASN N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 317 Processing helix chain 'N' and resid 347 through 363 Processing helix chain 'N' and resid 365 through 370 Processing helix chain 'N' and resid 396 through 403 Processing helix chain 'N' and resid 403 through 419 Processing helix chain 'N' and resid 420 through 422 No H-bonds generated for 'chain 'N' and resid 420 through 422' Processing helix chain 'N' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN N 450 " --> pdb=" O LYS N 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE N 451 " --> pdb=" O LEU N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 462 Processing helix chain 'N' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN N 480 " --> pdb=" O ALA N 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS N 495 " --> pdb=" O TYR N 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN N 496 " --> pdb=" O ASN N 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS N 497 " --> pdb=" O ASP N 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU N 498 " --> pdb=" O GLY N 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 46 Processing helix chain 'O' and resid 48 through 56 removed outlier: 3.693A pdb=" N VAL O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR O 75 " --> pdb=" O GLY O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 112 Processing helix chain 'O' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU O 224 " --> pdb=" O PRO O 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU O 234 " --> pdb=" O TYR O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 241 through 243 No H-bonds generated for 'chain 'O' and resid 241 through 243' Processing helix chain 'O' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU O 286 " --> pdb=" O GLU O 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP O 289 " --> pdb=" O LYS O 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA O 293 " --> pdb=" O ASP O 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE O 295 " --> pdb=" O LEU O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE P 91 " --> pdb=" O VAL P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET P 110 " --> pdb=" O ASN P 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR P 111 " --> pdb=" O GLN P 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS P 112 " --> pdb=" O VAL P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 153 Processing helix chain 'P' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG P 173 " --> pdb=" O LYS P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 204 No H-bonds generated for 'chain 'P' and resid 202 through 204' Processing helix chain 'P' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE P 281 " --> pdb=" O PHE P 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE P 282 " --> pdb=" O ASN P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 317 Processing helix chain 'P' and resid 347 through 363 Processing helix chain 'P' and resid 365 through 370 Processing helix chain 'P' and resid 396 through 403 Processing helix chain 'P' and resid 403 through 419 Processing helix chain 'P' and resid 420 through 422 No H-bonds generated for 'chain 'P' and resid 420 through 422' Processing helix chain 'P' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN P 450 " --> pdb=" O LYS P 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE P 451 " --> pdb=" O LEU P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 462 Processing helix chain 'P' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS P 495 " --> pdb=" O TYR P 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN P 496 " --> pdb=" O ASN P 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS P 497 " --> pdb=" O ASP P 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU P 498 " --> pdb=" O GLY P 494 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 46 Processing helix chain 'Q' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR Q 75 " --> pdb=" O GLY Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 Processing helix chain 'Q' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU Q 224 " --> pdb=" O PRO Q 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU Q 234 " --> pdb=" O TYR Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 241 through 243 No H-bonds generated for 'chain 'Q' and resid 241 through 243' Processing helix chain 'Q' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU Q 286 " --> pdb=" O GLU Q 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP Q 289 " --> pdb=" O LYS Q 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA Q 293 " --> pdb=" O ASP Q 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR Q 294 " --> pdb=" O GLY Q 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Q 295 " --> pdb=" O LEU Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS R 90 " --> pdb=" O ASP R 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET R 110 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR R 111 " --> pdb=" O GLN R 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS R 112 " --> pdb=" O VAL R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 153 Processing helix chain 'R' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG R 173 " --> pdb=" O LYS R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE R 282 " --> pdb=" O ASN R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 317 Processing helix chain 'R' and resid 347 through 363 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 396 through 403 Processing helix chain 'R' and resid 403 through 419 Processing helix chain 'R' and resid 420 through 422 No H-bonds generated for 'chain 'R' and resid 420 through 422' Processing helix chain 'R' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN R 450 " --> pdb=" O LYS R 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE R 451 " --> pdb=" O LEU R 447 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 462 Processing helix chain 'R' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN R 480 " --> pdb=" O ALA R 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS R 495 " --> pdb=" O TYR R 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN R 496 " --> pdb=" O ASN R 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS R 497 " --> pdb=" O ASP R 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU R 498 " --> pdb=" O GLY R 494 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 46 Processing helix chain 'S' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL S 52 " --> pdb=" O SER S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR S 75 " --> pdb=" O GLY S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 112 Processing helix chain 'S' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU S 224 " --> pdb=" O PRO S 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU S 234 " --> pdb=" O TYR S 230 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 243 No H-bonds generated for 'chain 'S' and resid 241 through 243' Processing helix chain 'S' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU S 286 " --> pdb=" O GLU S 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP S 289 " --> pdb=" O LYS S 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA S 293 " --> pdb=" O ASP S 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR S 294 " --> pdb=" O GLY S 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE S 295 " --> pdb=" O LEU S 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS T 90 " --> pdb=" O ASP T 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE T 91 " --> pdb=" O VAL T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET T 110 " --> pdb=" O ASN T 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR T 111 " --> pdb=" O GLN T 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS T 112 " --> pdb=" O VAL T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 153 Processing helix chain 'T' and resid 163 through 178 removed outlier: 3.576A pdb=" N ARG T 173 " --> pdb=" O LYS T 169 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 204 No H-bonds generated for 'chain 'T' and resid 202 through 204' Processing helix chain 'T' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE T 263 " --> pdb=" O SER T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE T 281 " --> pdb=" O PHE T 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE T 282 " --> pdb=" O ASN T 278 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 317 Processing helix chain 'T' and resid 347 through 363 Processing helix chain 'T' and resid 365 through 370 Processing helix chain 'T' and resid 396 through 403 Processing helix chain 'T' and resid 403 through 419 Processing helix chain 'T' and resid 420 through 422 No H-bonds generated for 'chain 'T' and resid 420 through 422' Processing helix chain 'T' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN T 450 " --> pdb=" O LYS T 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE T 451 " --> pdb=" O LEU T 447 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 462 Processing helix chain 'T' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN T 480 " --> pdb=" O ALA T 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS T 495 " --> pdb=" O TYR T 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN T 496 " --> pdb=" O ASN T 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS T 497 " --> pdb=" O ASP T 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU T 498 " --> pdb=" O GLY T 494 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN U 39 " --> pdb=" O SER U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 48 through 56 removed outlier: 3.693A pdb=" N VAL U 52 " --> pdb=" O SER U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR U 75 " --> pdb=" O GLY U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 112 Processing helix chain 'U' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU U 224 " --> pdb=" O PRO U 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU U 234 " --> pdb=" O TYR U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 243 No H-bonds generated for 'chain 'U' and resid 241 through 243' Processing helix chain 'U' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU U 286 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP U 289 " --> pdb=" O LYS U 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA U 293 " --> pdb=" O ASP U 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR U 294 " --> pdb=" O GLY U 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE U 295 " --> pdb=" O LEU U 291 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 92 removed outlier: 3.666A pdb=" N LYS V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE V 91 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 112 removed outlier: 3.739A pdb=" N MET V 110 " --> pdb=" O ASN V 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR V 111 " --> pdb=" O GLN V 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS V 112 " --> pdb=" O VAL V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 153 Processing helix chain 'V' and resid 163 through 178 removed outlier: 3.577A pdb=" N ARG V 173 " --> pdb=" O LYS V 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 259 through 264 removed outlier: 3.622A pdb=" N ILE V 263 " --> pdb=" O SER V 259 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 284 removed outlier: 4.007A pdb=" N PHE V 281 " --> pdb=" O PHE V 277 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE V 282 " --> pdb=" O ASN V 278 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 317 Processing helix chain 'V' and resid 347 through 363 Processing helix chain 'V' and resid 365 through 370 Processing helix chain 'V' and resid 396 through 403 Processing helix chain 'V' and resid 403 through 419 Processing helix chain 'V' and resid 420 through 422 No H-bonds generated for 'chain 'V' and resid 420 through 422' Processing helix chain 'V' and resid 434 through 452 removed outlier: 3.959A pdb=" N GLN V 450 " --> pdb=" O LYS V 446 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE V 451 " --> pdb=" O LEU V 447 " (cutoff:3.500A) Processing helix chain 'V' and resid 454 through 462 Processing helix chain 'V' and resid 475 through 502 removed outlier: 3.583A pdb=" N GLN V 480 " --> pdb=" O ALA V 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS V 495 " --> pdb=" O TYR V 491 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN V 496 " --> pdb=" O ASN V 492 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS V 497 " --> pdb=" O ASP V 493 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU V 498 " --> pdb=" O GLY V 494 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 40 removed outlier: 3.920A pdb=" N ASN X 39 " --> pdb=" O SER X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 46 Processing helix chain 'X' and resid 48 through 56 removed outlier: 3.692A pdb=" N VAL X 52 " --> pdb=" O SER X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 90 removed outlier: 3.667A pdb=" N TYR X 75 " --> pdb=" O GLY X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 112 Processing helix chain 'X' and resid 220 through 240 removed outlier: 3.958A pdb=" N GLU X 224 " --> pdb=" O PRO X 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU X 234 " --> pdb=" O TYR X 230 " (cutoff:3.500A) Processing helix chain 'X' and resid 241 through 243 No H-bonds generated for 'chain 'X' and resid 241 through 243' Processing helix chain 'X' and resid 273 through 296 removed outlier: 3.630A pdb=" N GLU X 286 " --> pdb=" O GLU X 282 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP X 289 " --> pdb=" O LYS X 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA X 293 " --> pdb=" O ASP X 289 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR X 294 " --> pdb=" O GLY X 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE X 295 " --> pdb=" O LEU X 291 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR A 208 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG A 222 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 233 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 227 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 123 through 128 Processing sheet with id=3, first strand: chain 'A' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN A 182 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 290 through 294 Processing sheet with id=5, first strand: chain 'W' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR W 105 " --> pdb=" O GLN W 195 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN W 195 " --> pdb=" O TYR W 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET W 196 " --> pdb=" O GLN W 132 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL W 202 " --> pdb=" O VAL W 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL W 126 " --> pdb=" O VAL W 202 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'W' and resid 116 through 117 Processing sheet with id=7, first strand: chain 'W' and resid 250 through 255 Processing sheet with id=8, first strand: chain 'B' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR B 208 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG B 222 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 233 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 227 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 123 through 128 Processing sheet with id=10, first strand: chain 'B' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN B 182 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 290 through 294 Processing sheet with id=12, first strand: chain 'C' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR C 105 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C 195 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET C 196 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 202 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 126 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=14, first strand: chain 'C' and resid 250 through 255 Processing sheet with id=15, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR D 208 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 222 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 233 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 227 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 123 through 128 Processing sheet with id=17, first strand: chain 'D' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN D 182 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 290 through 294 Processing sheet with id=19, first strand: chain 'E' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR E 105 " --> pdb=" O GLN E 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN E 195 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET E 196 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL E 202 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL E 126 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 116 through 117 Processing sheet with id=21, first strand: chain 'E' and resid 250 through 255 Processing sheet with id=22, first strand: chain 'F' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR F 208 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG F 222 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 233 " --> pdb=" O GLN F 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL F 227 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'F' and resid 123 through 128 Processing sheet with id=24, first strand: chain 'F' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN F 182 " --> pdb=" O VAL F 201 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'F' and resid 290 through 294 Processing sheet with id=26, first strand: chain 'G' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR G 105 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN G 195 " --> pdb=" O TYR G 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET G 196 " --> pdb=" O GLN G 132 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL G 202 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL G 126 " --> pdb=" O VAL G 202 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 116 through 117 Processing sheet with id=28, first strand: chain 'G' and resid 250 through 255 Processing sheet with id=29, first strand: chain 'H' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR H 208 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG H 222 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA H 233 " --> pdb=" O GLN H 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL H 227 " --> pdb=" O VAL H 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL H 231 " --> pdb=" O VAL H 227 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 123 through 128 Processing sheet with id=31, first strand: chain 'H' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN H 182 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 290 through 294 Processing sheet with id=33, first strand: chain 'I' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR I 105 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN I 195 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET I 196 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL I 202 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL I 126 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 116 through 117 Processing sheet with id=35, first strand: chain 'I' and resid 250 through 255 Processing sheet with id=36, first strand: chain 'J' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR J 208 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG J 222 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 233 " --> pdb=" O GLN J 225 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL J 227 " --> pdb=" O VAL J 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL J 231 " --> pdb=" O VAL J 227 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'J' and resid 123 through 128 Processing sheet with id=38, first strand: chain 'J' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN J 182 " --> pdb=" O VAL J 201 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'J' and resid 290 through 294 Processing sheet with id=40, first strand: chain 'K' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR K 105 " --> pdb=" O GLN K 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN K 195 " --> pdb=" O TYR K 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET K 196 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL K 202 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL K 126 " --> pdb=" O VAL K 202 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 116 through 117 Processing sheet with id=42, first strand: chain 'K' and resid 250 through 255 Processing sheet with id=43, first strand: chain 'L' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR L 208 " --> pdb=" O ARG L 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG L 222 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA L 233 " --> pdb=" O GLN L 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL L 227 " --> pdb=" O VAL L 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL L 231 " --> pdb=" O VAL L 227 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'L' and resid 123 through 128 Processing sheet with id=45, first strand: chain 'L' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN L 182 " --> pdb=" O VAL L 201 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'L' and resid 290 through 294 Processing sheet with id=47, first strand: chain 'M' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR M 105 " --> pdb=" O GLN M 195 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN M 195 " --> pdb=" O TYR M 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET M 196 " --> pdb=" O GLN M 132 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL M 202 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL M 126 " --> pdb=" O VAL M 202 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=49, first strand: chain 'M' and resid 250 through 255 Processing sheet with id=50, first strand: chain 'N' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR N 208 " --> pdb=" O ARG N 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG N 222 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA N 233 " --> pdb=" O GLN N 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL N 227 " --> pdb=" O VAL N 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL N 231 " --> pdb=" O VAL N 227 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'N' and resid 123 through 128 Processing sheet with id=52, first strand: chain 'N' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN N 182 " --> pdb=" O VAL N 201 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'N' and resid 290 through 294 Processing sheet with id=54, first strand: chain 'O' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR O 105 " --> pdb=" O GLN O 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN O 195 " --> pdb=" O TYR O 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET O 196 " --> pdb=" O GLN O 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL O 202 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL O 126 " --> pdb=" O VAL O 202 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'O' and resid 116 through 117 Processing sheet with id=56, first strand: chain 'O' and resid 250 through 255 Processing sheet with id=57, first strand: chain 'P' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR P 208 " --> pdb=" O ARG P 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG P 222 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA P 233 " --> pdb=" O GLN P 225 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL P 227 " --> pdb=" O VAL P 231 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL P 231 " --> pdb=" O VAL P 227 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'P' and resid 123 through 128 Processing sheet with id=59, first strand: chain 'P' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN P 182 " --> pdb=" O VAL P 201 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'P' and resid 290 through 294 Processing sheet with id=61, first strand: chain 'Q' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR Q 105 " --> pdb=" O GLN Q 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN Q 195 " --> pdb=" O TYR Q 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET Q 196 " --> pdb=" O GLN Q 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL Q 202 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL Q 126 " --> pdb=" O VAL Q 202 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'Q' and resid 116 through 117 Processing sheet with id=63, first strand: chain 'Q' and resid 250 through 255 Processing sheet with id=64, first strand: chain 'R' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR R 208 " --> pdb=" O ARG R 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG R 222 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 233 " --> pdb=" O GLN R 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL R 227 " --> pdb=" O VAL R 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL R 231 " --> pdb=" O VAL R 227 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'R' and resid 123 through 128 Processing sheet with id=66, first strand: chain 'R' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN R 182 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'R' and resid 290 through 294 Processing sheet with id=68, first strand: chain 'S' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR S 105 " --> pdb=" O GLN S 195 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN S 195 " --> pdb=" O TYR S 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET S 196 " --> pdb=" O GLN S 132 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL S 202 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL S 126 " --> pdb=" O VAL S 202 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'S' and resid 116 through 117 Processing sheet with id=70, first strand: chain 'S' and resid 250 through 255 Processing sheet with id=71, first strand: chain 'T' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR T 208 " --> pdb=" O ARG T 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG T 222 " --> pdb=" O ALA T 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA T 233 " --> pdb=" O GLN T 225 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL T 227 " --> pdb=" O VAL T 231 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL T 231 " --> pdb=" O VAL T 227 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'T' and resid 123 through 128 Processing sheet with id=73, first strand: chain 'T' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN T 182 " --> pdb=" O VAL T 201 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'T' and resid 290 through 294 Processing sheet with id=75, first strand: chain 'U' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR U 105 " --> pdb=" O GLN U 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN U 195 " --> pdb=" O TYR U 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET U 196 " --> pdb=" O GLN U 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL U 202 " --> pdb=" O VAL U 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL U 126 " --> pdb=" O VAL U 202 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'U' and resid 116 through 117 Processing sheet with id=77, first strand: chain 'U' and resid 250 through 255 Processing sheet with id=78, first strand: chain 'V' and resid 71 through 72 removed outlier: 4.297A pdb=" N TYR V 208 " --> pdb=" O ARG V 72 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG V 222 " --> pdb=" O ALA V 209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA V 233 " --> pdb=" O GLN V 225 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL V 227 " --> pdb=" O VAL V 231 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL V 231 " --> pdb=" O VAL V 227 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'V' and resid 123 through 128 Processing sheet with id=80, first strand: chain 'V' and resid 195 through 201 removed outlier: 4.228A pdb=" N ASN V 182 " --> pdb=" O VAL V 201 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'V' and resid 290 through 294 Processing sheet with id=82, first strand: chain 'X' and resid 97 through 106 removed outlier: 6.713A pdb=" N TYR X 105 " --> pdb=" O GLN X 195 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN X 195 " --> pdb=" O TYR X 105 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET X 196 " --> pdb=" O GLN X 132 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL X 202 " --> pdb=" O VAL X 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL X 126 " --> pdb=" O VAL X 202 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'X' and resid 116 through 117 Processing sheet with id=84, first strand: chain 'X' and resid 250 through 255 2940 hydrogen bonds defined for protein. 8388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.36 Time building geometry restraints manager: 14.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22380 1.34 - 1.46: 13542 1.46 - 1.58: 32658 1.58 - 1.69: 0 1.69 - 1.81: 528 Bond restraints: 69108 Sorted by residual: bond pdb=" CB ILE I 244 " pdb=" CG2 ILE I 244 " ideal model delta sigma weight residual 1.521 1.554 -0.033 3.30e-02 9.18e+02 9.95e-01 bond pdb=" CB ILE C 244 " pdb=" CG2 ILE C 244 " ideal model delta sigma weight residual 1.521 1.554 -0.033 3.30e-02 9.18e+02 9.95e-01 bond pdb=" CB ILE G 244 " pdb=" CG2 ILE G 244 " ideal model delta sigma weight residual 1.521 1.554 -0.033 3.30e-02 9.18e+02 9.92e-01 bond pdb=" CB ILE M 244 " pdb=" CG2 ILE M 244 " ideal model delta sigma weight residual 1.521 1.554 -0.033 3.30e-02 9.18e+02 9.92e-01 bond pdb=" CB ILE W 244 " pdb=" CG2 ILE W 244 " ideal model delta sigma weight residual 1.521 1.554 -0.033 3.30e-02 9.18e+02 9.92e-01 ... (remaining 69103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 87094 0.96 - 1.92: 5150 1.92 - 2.87: 562 2.87 - 3.83: 266 3.83 - 4.79: 132 Bond angle restraints: 93204 Sorted by residual: angle pdb=" CA TRP E 146 " pdb=" CB TRP E 146 " pdb=" CG TRP E 146 " ideal model delta sigma weight residual 113.60 117.43 -3.83 1.90e+00 2.77e-01 4.06e+00 angle pdb=" CA TRP X 146 " pdb=" CB TRP X 146 " pdb=" CG TRP X 146 " ideal model delta sigma weight residual 113.60 117.43 -3.83 1.90e+00 2.77e-01 4.06e+00 angle pdb=" CA TRP K 146 " pdb=" CB TRP K 146 " pdb=" CG TRP K 146 " ideal model delta sigma weight residual 113.60 117.43 -3.83 1.90e+00 2.77e-01 4.06e+00 angle pdb=" CA TRP Q 146 " pdb=" CB TRP Q 146 " pdb=" CG TRP Q 146 " ideal model delta sigma weight residual 113.60 117.43 -3.83 1.90e+00 2.77e-01 4.06e+00 angle pdb=" CA TRP G 146 " pdb=" CB TRP G 146 " pdb=" CG TRP G 146 " ideal model delta sigma weight residual 113.60 117.42 -3.82 1.90e+00 2.77e-01 4.04e+00 ... (remaining 93199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 37696 16.86 - 33.72: 3164 33.72 - 50.59: 528 50.59 - 67.45: 240 67.45 - 84.31: 108 Dihedral angle restraints: 41736 sinusoidal: 17472 harmonic: 24264 Sorted by residual: dihedral pdb=" CA GLU G 149 " pdb=" C GLU G 149 " pdb=" N HIS G 150 " pdb=" CA HIS G 150 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU W 149 " pdb=" C GLU W 149 " pdb=" N HIS W 150 " pdb=" CA HIS W 150 " ideal model delta harmonic sigma weight residual 180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU M 149 " pdb=" C GLU M 149 " pdb=" N HIS M 150 " pdb=" CA HIS M 150 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 41733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 6190 0.030 - 0.061: 2522 0.061 - 0.091: 592 0.091 - 0.122: 420 0.122 - 0.152: 116 Chirality restraints: 9840 Sorted by residual: chirality pdb=" CA ILE F 325 " pdb=" N ILE F 325 " pdb=" C ILE F 325 " pdb=" CB ILE F 325 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE L 325 " pdb=" N ILE L 325 " pdb=" C ILE L 325 " pdb=" CB ILE L 325 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 9837 not shown) Planarity restraints: 12240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 233 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C LYS K 233 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS K 233 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU K 234 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 233 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C LYS Q 233 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS Q 233 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU Q 234 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS X 233 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C LYS X 233 " -0.046 2.00e-02 2.50e+03 pdb=" O LYS X 233 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU X 234 " 0.015 2.00e-02 2.50e+03 ... (remaining 12237 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 21048 2.83 - 3.35: 64372 3.35 - 3.86: 107132 3.86 - 4.38: 124570 4.38 - 4.90: 217660 Nonbonded interactions: 534782 Sorted by model distance: nonbonded pdb=" NH1 ARG N 248 " pdb=" OG SER N 253 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG T 248 " pdb=" OG SER T 253 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG H 248 " pdb=" OG SER H 253 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG B 248 " pdb=" OG SER B 253 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG D 248 " pdb=" OG SER D 253 " model vdw 2.311 3.120 ... (remaining 534777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 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: 1.880 Check model and map are aligned: 0.390 Set scattering table: 0.460 Process input model: 108.130 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.280 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.003 0.033 69108 Z= 0.204 Angle : 0.535 4.788 93204 Z= 0.287 Chirality : 0.041 0.152 9840 Planarity : 0.004 0.037 12240 Dihedral : 13.883 84.309 26184 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.52 (0.09), residues: 8280 helix: 1.50 (0.09), residues: 3120 sheet: -1.69 (0.13), residues: 1308 loop : 0.30 (0.10), residues: 3852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 146 HIS 0.012 0.001 HIS S 77 PHE 0.012 0.001 PHE H 124 TYR 0.010 0.001 TYR Q 294 ARG 0.004 0.000 ARG P 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2600 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2600 time to evaluate : 5.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7481 (tt0) cc_final: 0.7177 (tt0) REVERT: A 143 MET cc_start: 0.7942 (mtm) cc_final: 0.7740 (mtm) REVERT: A 182 ASN cc_start: 0.8287 (m110) cc_final: 0.7413 (m-40) REVERT: A 187 PHE cc_start: 0.8806 (m-80) cc_final: 0.8570 (m-80) REVERT: A 242 MET cc_start: 0.8583 (tpp) cc_final: 0.8382 (tpt) REVERT: A 247 PRO cc_start: 0.9298 (Cg_endo) cc_final: 0.8956 (Cg_exo) REVERT: A 279 ASP cc_start: 0.7813 (t70) cc_final: 0.7582 (t0) REVERT: A 300 GLN cc_start: 0.7268 (mt0) cc_final: 0.6914 (mt0) REVERT: A 498 GLU cc_start: 0.7347 (tp30) cc_final: 0.6918 (tp30) REVERT: W 144 ASN cc_start: 0.8477 (p0) cc_final: 0.8093 (p0) REVERT: W 217 TRP cc_start: 0.8794 (p90) cc_final: 0.8322 (p90) REVERT: W 234 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7934 (mm-30) REVERT: W 242 LEU cc_start: 0.9236 (mt) cc_final: 0.8985 (mt) REVERT: B 117 TYR cc_start: 0.7182 (m-10) cc_final: 0.6796 (m-10) REVERT: B 130 ASP cc_start: 0.8143 (m-30) cc_final: 0.7460 (p0) REVERT: B 141 GLU cc_start: 0.6916 (tp30) cc_final: 0.6608 (tp30) REVERT: B 222 ARG cc_start: 0.9000 (ttt90) cc_final: 0.8695 (ttm-80) REVERT: B 242 MET cc_start: 0.8510 (tpp) cc_final: 0.8212 (tpt) REVERT: B 247 PRO cc_start: 0.9305 (Cg_endo) cc_final: 0.8955 (Cg_exo) REVERT: B 279 ASP cc_start: 0.7989 (t70) cc_final: 0.7667 (t0) REVERT: B 445 LEU cc_start: 0.8415 (tp) cc_final: 0.8061 (tp) REVERT: B 498 GLU cc_start: 0.7474 (tp30) cc_final: 0.7172 (tp30) REVERT: C 132 GLN cc_start: 0.7959 (pt0) cc_final: 0.7753 (pt0) REVERT: C 149 GLU cc_start: 0.7051 (tt0) cc_final: 0.6747 (tt0) REVERT: C 196 MET cc_start: 0.8577 (tpt) cc_final: 0.8198 (tpt) REVERT: C 217 TRP cc_start: 0.8750 (p90) cc_final: 0.8353 (p90) REVERT: C 234 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 270 TYR cc_start: 0.7027 (m-80) cc_final: 0.6229 (m-10) REVERT: D 112 CYS cc_start: 0.7260 (t) cc_final: 0.7045 (t) REVERT: D 117 TYR cc_start: 0.7155 (m-10) cc_final: 0.6948 (m-10) REVERT: D 182 ASN cc_start: 0.8333 (m110) cc_final: 0.7500 (m-40) REVERT: D 187 PHE cc_start: 0.8752 (m-80) cc_final: 0.8458 (m-80) REVERT: D 222 ARG cc_start: 0.8928 (ttt90) cc_final: 0.8635 (ttm-80) REVERT: D 234 SER cc_start: 0.8730 (p) cc_final: 0.8478 (p) REVERT: D 242 MET cc_start: 0.8555 (tpp) cc_final: 0.8332 (tpt) REVERT: D 247 PRO cc_start: 0.9282 (Cg_endo) cc_final: 0.8951 (Cg_exo) REVERT: D 279 ASP cc_start: 0.8011 (t70) cc_final: 0.7669 (t0) REVERT: D 324 GLN cc_start: 0.7512 (mt0) cc_final: 0.7225 (mt0) REVERT: D 329 MET cc_start: 0.8584 (mtp) cc_final: 0.8362 (mtm) REVERT: D 426 TYR cc_start: 0.8015 (m-80) cc_final: 0.7805 (m-10) REVERT: E 132 GLN cc_start: 0.8086 (pt0) cc_final: 0.7813 (pt0) REVERT: E 144 ASN cc_start: 0.8426 (p0) cc_final: 0.8160 (p0) REVERT: E 196 MET cc_start: 0.8577 (tpt) cc_final: 0.8236 (tpt) REVERT: E 217 TRP cc_start: 0.8825 (p90) cc_final: 0.8390 (p90) REVERT: F 59 GLU cc_start: 0.7488 (tt0) cc_final: 0.7182 (tt0) REVERT: F 143 MET cc_start: 0.7945 (mtm) cc_final: 0.7741 (mtm) REVERT: F 182 ASN cc_start: 0.8289 (m110) cc_final: 0.7418 (m-40) REVERT: F 187 PHE cc_start: 0.8805 (m-80) cc_final: 0.8568 (m-80) REVERT: F 247 PRO cc_start: 0.9296 (Cg_endo) cc_final: 0.8955 (Cg_exo) REVERT: F 279 ASP cc_start: 0.7797 (t70) cc_final: 0.7556 (t0) REVERT: F 300 GLN cc_start: 0.7264 (mt0) cc_final: 0.6910 (mt0) REVERT: F 498 GLU cc_start: 0.7343 (tp30) cc_final: 0.6913 (tp30) REVERT: G 144 ASN cc_start: 0.8457 (p0) cc_final: 0.8122 (p0) REVERT: G 217 TRP cc_start: 0.8800 (p90) cc_final: 0.8324 (p90) REVERT: G 234 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7931 (mm-30) REVERT: G 242 LEU cc_start: 0.9232 (mt) cc_final: 0.8983 (mt) REVERT: H 117 TYR cc_start: 0.7170 (m-10) cc_final: 0.6790 (m-10) REVERT: H 130 ASP cc_start: 0.8147 (m-30) cc_final: 0.7461 (p0) REVERT: H 141 GLU cc_start: 0.6924 (tp30) cc_final: 0.6617 (tp30) REVERT: H 222 ARG cc_start: 0.9003 (ttt90) cc_final: 0.8693 (ttm-80) REVERT: H 242 MET cc_start: 0.8511 (tpp) cc_final: 0.8215 (tpt) REVERT: H 247 PRO cc_start: 0.9301 (Cg_endo) cc_final: 0.8955 (Cg_exo) REVERT: H 279 ASP cc_start: 0.8012 (t70) cc_final: 0.7693 (t0) REVERT: H 445 LEU cc_start: 0.8417 (tp) cc_final: 0.8062 (tp) REVERT: H 498 GLU cc_start: 0.7470 (tp30) cc_final: 0.7168 (tp30) REVERT: I 149 GLU cc_start: 0.7042 (tt0) cc_final: 0.6752 (tt0) REVERT: I 196 MET cc_start: 0.8580 (tpt) cc_final: 0.8226 (tpt) REVERT: I 217 TRP cc_start: 0.8747 (p90) cc_final: 0.8348 (p90) REVERT: I 234 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7792 (mm-30) REVERT: I 270 TYR cc_start: 0.7039 (m-80) cc_final: 0.6227 (m-10) REVERT: J 112 CYS cc_start: 0.7253 (t) cc_final: 0.7043 (t) REVERT: J 117 TYR cc_start: 0.7154 (m-10) cc_final: 0.6953 (m-10) REVERT: J 182 ASN cc_start: 0.8334 (m110) cc_final: 0.7502 (m-40) REVERT: J 187 PHE cc_start: 0.8748 (m-80) cc_final: 0.8450 (m-80) REVERT: J 222 ARG cc_start: 0.8930 (ttt90) cc_final: 0.8637 (ttm-80) REVERT: J 234 SER cc_start: 0.8728 (p) cc_final: 0.8477 (p) REVERT: J 242 MET cc_start: 0.8558 (tpp) cc_final: 0.8332 (tpt) REVERT: J 247 PRO cc_start: 0.9279 (Cg_endo) cc_final: 0.8946 (Cg_exo) REVERT: J 279 ASP cc_start: 0.7993 (t70) cc_final: 0.7656 (t0) REVERT: J 324 GLN cc_start: 0.7535 (mt0) cc_final: 0.7228 (mt0) REVERT: J 329 MET cc_start: 0.8598 (mtp) cc_final: 0.8389 (mtm) REVERT: J 426 TYR cc_start: 0.8018 (m-80) cc_final: 0.7807 (m-10) REVERT: K 132 GLN cc_start: 0.8096 (pt0) cc_final: 0.7825 (pt0) REVERT: K 144 ASN cc_start: 0.8429 (p0) cc_final: 0.8157 (p0) REVERT: K 196 MET cc_start: 0.8592 (tpt) cc_final: 0.8254 (tpt) REVERT: K 217 TRP cc_start: 0.8819 (p90) cc_final: 0.8386 (p90) REVERT: L 59 GLU cc_start: 0.7483 (tt0) cc_final: 0.7190 (tt0) REVERT: L 182 ASN cc_start: 0.8284 (m110) cc_final: 0.7418 (m-40) REVERT: L 187 PHE cc_start: 0.8801 (m-80) cc_final: 0.8566 (m-80) REVERT: L 247 PRO cc_start: 0.9293 (Cg_endo) cc_final: 0.8951 (Cg_exo) REVERT: L 279 ASP cc_start: 0.7774 (t70) cc_final: 0.7541 (t0) REVERT: L 300 GLN cc_start: 0.7249 (mt0) cc_final: 0.6944 (mt0) REVERT: L 498 GLU cc_start: 0.7346 (tp30) cc_final: 0.6917 (tp30) REVERT: M 144 ASN cc_start: 0.8448 (p0) cc_final: 0.8109 (p0) REVERT: M 217 TRP cc_start: 0.8789 (p90) cc_final: 0.8322 (p90) REVERT: M 234 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7946 (mm-30) REVERT: M 242 LEU cc_start: 0.9234 (mt) cc_final: 0.8991 (mt) REVERT: N 117 TYR cc_start: 0.7174 (m-10) cc_final: 0.6799 (m-10) REVERT: N 130 ASP cc_start: 0.8142 (m-30) cc_final: 0.7463 (p0) REVERT: N 141 GLU cc_start: 0.6939 (tp30) cc_final: 0.6622 (tp30) REVERT: N 222 ARG cc_start: 0.9003 (ttt90) cc_final: 0.8688 (ttm-80) REVERT: N 242 MET cc_start: 0.8514 (tpp) cc_final: 0.8217 (tpt) REVERT: N 247 PRO cc_start: 0.9301 (Cg_endo) cc_final: 0.8954 (Cg_exo) REVERT: N 279 ASP cc_start: 0.8017 (t70) cc_final: 0.7696 (t0) REVERT: N 445 LEU cc_start: 0.8413 (tp) cc_final: 0.8059 (tp) REVERT: N 498 GLU cc_start: 0.7473 (tp30) cc_final: 0.7173 (tp30) REVERT: O 149 GLU cc_start: 0.7032 (tt0) cc_final: 0.6766 (tt0) REVERT: O 196 MET cc_start: 0.8583 (tpt) cc_final: 0.8208 (tpt) REVERT: O 217 TRP cc_start: 0.8748 (p90) cc_final: 0.8352 (p90) REVERT: O 234 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7810 (mm-30) REVERT: O 270 TYR cc_start: 0.7042 (m-80) cc_final: 0.6236 (m-10) REVERT: P 112 CYS cc_start: 0.7256 (t) cc_final: 0.7039 (t) REVERT: P 117 TYR cc_start: 0.7156 (m-10) cc_final: 0.6956 (m-10) REVERT: P 125 GLU cc_start: 0.8121 (tt0) cc_final: 0.7917 (tt0) REVERT: P 182 ASN cc_start: 0.8338 (m110) cc_final: 0.7506 (m-40) REVERT: P 187 PHE cc_start: 0.8747 (m-80) cc_final: 0.8451 (m-80) REVERT: P 222 ARG cc_start: 0.8934 (ttt90) cc_final: 0.8641 (ttm-80) REVERT: P 234 SER cc_start: 0.8729 (p) cc_final: 0.8477 (p) REVERT: P 242 MET cc_start: 0.8556 (tpp) cc_final: 0.8335 (tpt) REVERT: P 247 PRO cc_start: 0.9284 (Cg_endo) cc_final: 0.8952 (Cg_exo) REVERT: P 279 ASP cc_start: 0.7985 (t70) cc_final: 0.7666 (t0) REVERT: P 324 GLN cc_start: 0.7540 (mt0) cc_final: 0.7235 (mt0) REVERT: P 329 MET cc_start: 0.8602 (mtp) cc_final: 0.8383 (mtm) REVERT: P 426 TYR cc_start: 0.8015 (m-80) cc_final: 0.7806 (m-10) REVERT: Q 132 GLN cc_start: 0.8100 (pt0) cc_final: 0.7807 (pt0) REVERT: Q 144 ASN cc_start: 0.8423 (p0) cc_final: 0.8152 (p0) REVERT: Q 196 MET cc_start: 0.8592 (tpt) cc_final: 0.8242 (tpt) REVERT: Q 217 TRP cc_start: 0.8824 (p90) cc_final: 0.8385 (p90) REVERT: R 59 GLU cc_start: 0.7484 (tt0) cc_final: 0.7191 (tt0) REVERT: R 182 ASN cc_start: 0.8286 (m110) cc_final: 0.7423 (m-40) REVERT: R 187 PHE cc_start: 0.8799 (m-80) cc_final: 0.8567 (m-80) REVERT: R 247 PRO cc_start: 0.9293 (Cg_endo) cc_final: 0.8953 (Cg_exo) REVERT: R 279 ASP cc_start: 0.7790 (t70) cc_final: 0.7568 (t0) REVERT: R 300 GLN cc_start: 0.7255 (mt0) cc_final: 0.6944 (mt0) REVERT: R 498 GLU cc_start: 0.7350 (tp30) cc_final: 0.6921 (tp30) REVERT: S 144 ASN cc_start: 0.8464 (p0) cc_final: 0.8080 (p0) REVERT: S 217 TRP cc_start: 0.8785 (p90) cc_final: 0.8323 (p90) REVERT: S 234 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7954 (mm-30) REVERT: S 242 LEU cc_start: 0.9241 (mt) cc_final: 0.8996 (mt) REVERT: T 117 TYR cc_start: 0.7181 (m-10) cc_final: 0.6804 (m-10) REVERT: T 130 ASP cc_start: 0.8142 (m-30) cc_final: 0.7463 (p0) REVERT: T 141 GLU cc_start: 0.6933 (tp30) cc_final: 0.6620 (tp30) REVERT: T 222 ARG cc_start: 0.9001 (ttt90) cc_final: 0.8689 (ttm-80) REVERT: T 242 MET cc_start: 0.8514 (tpp) cc_final: 0.8215 (tpt) REVERT: T 247 PRO cc_start: 0.9302 (Cg_endo) cc_final: 0.8951 (Cg_exo) REVERT: T 279 ASP cc_start: 0.7997 (t70) cc_final: 0.7669 (t0) REVERT: T 445 LEU cc_start: 0.8414 (tp) cc_final: 0.8060 (tp) REVERT: T 498 GLU cc_start: 0.7471 (tp30) cc_final: 0.7170 (tp30) REVERT: U 62 GLN cc_start: 0.8349 (pt0) cc_final: 0.8115 (pt0) REVERT: U 149 GLU cc_start: 0.7041 (tt0) cc_final: 0.6766 (tt0) REVERT: U 196 MET cc_start: 0.8579 (tpt) cc_final: 0.8183 (tpt) REVERT: U 217 TRP cc_start: 0.8751 (p90) cc_final: 0.8357 (p90) REVERT: U 234 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7830 (mm-30) REVERT: U 270 TYR cc_start: 0.7031 (m-80) cc_final: 0.6231 (m-10) REVERT: V 112 CYS cc_start: 0.7263 (t) cc_final: 0.7049 (t) REVERT: V 117 TYR cc_start: 0.7163 (m-10) cc_final: 0.6960 (m-10) REVERT: V 125 GLU cc_start: 0.8123 (tt0) cc_final: 0.7921 (tt0) REVERT: V 182 ASN cc_start: 0.8335 (m110) cc_final: 0.7495 (m-40) REVERT: V 187 PHE cc_start: 0.8754 (m-80) cc_final: 0.8459 (m-80) REVERT: V 222 ARG cc_start: 0.8931 (ttt90) cc_final: 0.8643 (ttm-80) REVERT: V 234 SER cc_start: 0.8735 (p) cc_final: 0.8485 (p) REVERT: V 242 MET cc_start: 0.8559 (tpp) cc_final: 0.8334 (tpt) REVERT: V 247 PRO cc_start: 0.9282 (Cg_endo) cc_final: 0.8951 (Cg_exo) REVERT: V 279 ASP cc_start: 0.7998 (t70) cc_final: 0.7679 (t0) REVERT: V 324 GLN cc_start: 0.7519 (mt0) cc_final: 0.7233 (mt0) REVERT: V 329 MET cc_start: 0.8583 (mtp) cc_final: 0.8345 (mtm) REVERT: V 426 TYR cc_start: 0.8023 (m-80) cc_final: 0.7812 (m-10) REVERT: X 132 GLN cc_start: 0.8095 (pt0) cc_final: 0.7809 (pt0) REVERT: X 144 ASN cc_start: 0.8424 (p0) cc_final: 0.8154 (p0) REVERT: X 196 MET cc_start: 0.8581 (tpt) cc_final: 0.8229 (tpt) REVERT: X 217 TRP cc_start: 0.8825 (p90) cc_final: 0.8387 (p90) outliers start: 0 outliers final: 0 residues processed: 2600 average time/residue: 0.6698 time to fit residues: 2869.3905 Evaluate side-chains 1870 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1870 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 689 optimal weight: 5.9990 chunk 618 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 417 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 639 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 741 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 HIS ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 ASN B 55 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 214 ASN D 55 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 214 ASN F 55 GLN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 ASN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN H 55 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** H 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 279 GLN J 55 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 HIS K 214 ASN L 55 GLN ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 356 ASN ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 ASN N 55 GLN ** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 ASN ** N 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN O 279 GLN ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 HIS Q 214 ASN R 55 GLN ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 356 ASN ** R 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 HIS ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN ** T 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 214 ASN V 55 GLN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 HIS X 214 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 69108 Z= 0.605 Angle : 0.810 14.045 93204 Z= 0.432 Chirality : 0.052 0.182 9840 Planarity : 0.005 0.041 12240 Dihedral : 5.760 21.330 9120 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.33 % Allowed : 4.13 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.23 (0.09), residues: 8280 helix: 0.68 (0.09), residues: 3120 sheet: -1.78 (0.13), residues: 1260 loop : -0.10 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP G 217 HIS 0.007 0.002 HIS P 303 PHE 0.025 0.003 PHE D 187 TYR 0.021 0.003 TYR M 294 ARG 0.009 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1958 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1934 time to evaluate : 5.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.7442 (m-80) cc_final: 0.6524 (m-80) REVERT: A 176 TYR cc_start: 0.8944 (m-10) cc_final: 0.8734 (m-80) REVERT: A 182 ASN cc_start: 0.8436 (m110) cc_final: 0.8177 (m-40) REVERT: A 306 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7449 (tm-30) REVERT: A 453 LYS cc_start: 0.8536 (ttmm) cc_final: 0.7679 (ttmt) REVERT: W 33 ASP cc_start: 0.7741 (t0) cc_final: 0.6933 (t0) REVERT: W 36 GLU cc_start: 0.8943 (mp0) cc_final: 0.7634 (mp0) REVERT: W 97 ASP cc_start: 0.8239 (t0) cc_final: 0.8025 (t0) REVERT: W 149 GLU cc_start: 0.7741 (tt0) cc_final: 0.7525 (tt0) REVERT: W 242 LEU cc_start: 0.9281 (mt) cc_final: 0.8923 (mt) REVERT: W 282 GLU cc_start: 0.7509 (tt0) cc_final: 0.7231 (tt0) REVERT: W 299 MET cc_start: 0.8425 (ttm) cc_final: 0.8215 (ttm) REVERT: B 111 TYR cc_start: 0.8881 (m-80) cc_final: 0.8543 (m-80) REVERT: B 152 ASN cc_start: 0.8225 (m-40) cc_final: 0.7703 (m110) REVERT: B 161 ARG cc_start: 0.7192 (ttp-170) cc_final: 0.6673 (ttp-170) REVERT: B 176 TYR cc_start: 0.8898 (m-10) cc_final: 0.8539 (m-10) REVERT: B 182 ASN cc_start: 0.8412 (m110) cc_final: 0.7721 (m-40) REVERT: B 242 MET cc_start: 0.8891 (tpp) cc_final: 0.8648 (tpt) REVERT: B 306 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8024 (tm-30) REVERT: B 426 TYR cc_start: 0.8334 (m-80) cc_final: 0.8107 (m-80) REVERT: C 36 GLU cc_start: 0.8790 (mp0) cc_final: 0.8491 (mp0) REVERT: C 97 ASP cc_start: 0.8424 (t0) cc_final: 0.8142 (t0) REVERT: C 110 PHE cc_start: 0.9235 (t80) cc_final: 0.9024 (t80) REVERT: C 196 MET cc_start: 0.8830 (tpt) cc_final: 0.8464 (tpt) REVERT: C 219 MET cc_start: 0.8703 (ttm) cc_final: 0.8323 (ttm) REVERT: C 254 GLU cc_start: 0.6411 (tt0) cc_final: 0.6181 (tt0) REVERT: C 282 GLU cc_start: 0.7230 (tt0) cc_final: 0.6845 (tt0) REVERT: D 71 PHE cc_start: 0.8516 (p90) cc_final: 0.8230 (p90) REVERT: D 93 ASN cc_start: 0.8004 (t0) cc_final: 0.7705 (t0) REVERT: D 100 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8881 (mp) REVERT: D 112 CYS cc_start: 0.7535 (t) cc_final: 0.7226 (t) REVERT: D 129 ARG cc_start: 0.7793 (tpt-90) cc_final: 0.7587 (tpt-90) REVERT: D 182 ASN cc_start: 0.8389 (m110) cc_final: 0.7685 (m-40) REVERT: D 196 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7025 (mt-10) REVERT: D 300 GLN cc_start: 0.7451 (mt0) cc_final: 0.6992 (mt0) REVERT: D 306 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7619 (tm-30) REVERT: D 329 MET cc_start: 0.8732 (mtp) cc_final: 0.8407 (mtt) REVERT: E 34 VAL cc_start: 0.9032 (m) cc_final: 0.8781 (t) REVERT: E 97 ASP cc_start: 0.8192 (t0) cc_final: 0.7919 (t0) REVERT: E 107 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 132 GLN cc_start: 0.8220 (pt0) cc_final: 0.7985 (pt0) REVERT: E 196 MET cc_start: 0.8760 (tpt) cc_final: 0.8444 (tpt) REVERT: E 222 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8163 (mp0) REVERT: E 282 GLU cc_start: 0.7644 (tt0) cc_final: 0.7222 (tt0) REVERT: E 299 MET cc_start: 0.8377 (ttm) cc_final: 0.8137 (ttp) REVERT: F 117 TYR cc_start: 0.7430 (m-80) cc_final: 0.6534 (m-80) REVERT: F 176 TYR cc_start: 0.8944 (m-10) cc_final: 0.8737 (m-80) REVERT: F 182 ASN cc_start: 0.8468 (m110) cc_final: 0.8106 (m-40) REVERT: F 306 GLU cc_start: 0.8654 (mm-30) cc_final: 0.7425 (tm-30) REVERT: F 453 LYS cc_start: 0.8534 (ttmm) cc_final: 0.7681 (ttmt) REVERT: G 33 ASP cc_start: 0.7742 (t0) cc_final: 0.6920 (t0) REVERT: G 36 GLU cc_start: 0.8946 (mp0) cc_final: 0.7631 (mp0) REVERT: G 149 GLU cc_start: 0.7729 (tt0) cc_final: 0.7510 (tt0) REVERT: G 242 LEU cc_start: 0.9277 (mt) cc_final: 0.8918 (mt) REVERT: G 282 GLU cc_start: 0.7513 (tt0) cc_final: 0.7239 (tt0) REVERT: G 299 MET cc_start: 0.8433 (ttm) cc_final: 0.8181 (ttm) REVERT: H 111 TYR cc_start: 0.8882 (m-80) cc_final: 0.8543 (m-80) REVERT: H 152 ASN cc_start: 0.8234 (m-40) cc_final: 0.7699 (m110) REVERT: H 161 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6670 (ttp-170) REVERT: H 176 TYR cc_start: 0.8905 (m-10) cc_final: 0.8540 (m-10) REVERT: H 182 ASN cc_start: 0.8404 (m110) cc_final: 0.7716 (m-40) REVERT: H 242 MET cc_start: 0.8900 (tpp) cc_final: 0.8652 (tpt) REVERT: H 306 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8020 (tm-30) REVERT: H 426 TYR cc_start: 0.8334 (m-80) cc_final: 0.8101 (m-80) REVERT: I 36 GLU cc_start: 0.8791 (mp0) cc_final: 0.8494 (mp0) REVERT: I 97 ASP cc_start: 0.8431 (t0) cc_final: 0.8145 (t0) REVERT: I 110 PHE cc_start: 0.9235 (t80) cc_final: 0.9029 (t80) REVERT: I 196 MET cc_start: 0.8864 (tpt) cc_final: 0.8523 (tpt) REVERT: I 219 MET cc_start: 0.8694 (ttm) cc_final: 0.8316 (ttm) REVERT: I 254 GLU cc_start: 0.6409 (tt0) cc_final: 0.6180 (tt0) REVERT: I 282 GLU cc_start: 0.7192 (tt0) cc_final: 0.6805 (tt0) REVERT: J 71 PHE cc_start: 0.8510 (p90) cc_final: 0.8223 (p90) REVERT: J 93 ASN cc_start: 0.8003 (t0) cc_final: 0.7707 (t0) REVERT: J 100 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8878 (mp) REVERT: J 112 CYS cc_start: 0.7543 (t) cc_final: 0.7227 (t) REVERT: J 182 ASN cc_start: 0.8385 (m110) cc_final: 0.7683 (m-40) REVERT: J 196 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7026 (mt-10) REVERT: J 300 GLN cc_start: 0.7449 (mt0) cc_final: 0.6995 (mt0) REVERT: J 306 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7605 (tm-30) REVERT: J 329 MET cc_start: 0.8751 (mtp) cc_final: 0.8439 (mtt) REVERT: J 453 LYS cc_start: 0.8291 (ttmm) cc_final: 0.8085 (ttmt) REVERT: K 34 VAL cc_start: 0.9026 (m) cc_final: 0.8770 (t) REVERT: K 97 ASP cc_start: 0.8185 (t0) cc_final: 0.7910 (t0) REVERT: K 107 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8040 (tm-30) REVERT: K 132 GLN cc_start: 0.8222 (pt0) cc_final: 0.7975 (pt0) REVERT: K 196 MET cc_start: 0.8774 (tpt) cc_final: 0.8452 (tpt) REVERT: K 222 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8163 (mp0) REVERT: K 282 GLU cc_start: 0.7658 (tt0) cc_final: 0.7231 (tt0) REVERT: K 299 MET cc_start: 0.8391 (ttm) cc_final: 0.8161 (ttp) REVERT: L 117 TYR cc_start: 0.7433 (m-80) cc_final: 0.6541 (m-80) REVERT: L 176 TYR cc_start: 0.8948 (m-10) cc_final: 0.8742 (m-80) REVERT: L 182 ASN cc_start: 0.8469 (m110) cc_final: 0.8109 (m-40) REVERT: L 306 GLU cc_start: 0.8653 (mm-30) cc_final: 0.7441 (tm-30) REVERT: L 453 LYS cc_start: 0.8534 (ttmm) cc_final: 0.7677 (ttmt) REVERT: M 33 ASP cc_start: 0.7742 (t0) cc_final: 0.6922 (t0) REVERT: M 36 GLU cc_start: 0.8945 (mp0) cc_final: 0.7637 (mp0) REVERT: M 149 GLU cc_start: 0.7746 (tt0) cc_final: 0.7536 (tt0) REVERT: M 242 LEU cc_start: 0.9280 (mt) cc_final: 0.8924 (mt) REVERT: M 282 GLU cc_start: 0.7546 (tt0) cc_final: 0.7253 (tt0) REVERT: M 299 MET cc_start: 0.8394 (ttm) cc_final: 0.8159 (ttm) REVERT: N 111 TYR cc_start: 0.8886 (m-80) cc_final: 0.8552 (m-80) REVERT: N 152 ASN cc_start: 0.8235 (m-40) cc_final: 0.7708 (m110) REVERT: N 161 ARG cc_start: 0.7194 (ttp-170) cc_final: 0.6671 (ttp-170) REVERT: N 176 TYR cc_start: 0.8902 (m-10) cc_final: 0.8532 (m-10) REVERT: N 182 ASN cc_start: 0.8416 (m110) cc_final: 0.7734 (m-40) REVERT: N 242 MET cc_start: 0.8897 (tpp) cc_final: 0.8647 (tpt) REVERT: N 306 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8019 (tm-30) REVERT: N 426 TYR cc_start: 0.8325 (m-80) cc_final: 0.8094 (m-80) REVERT: O 36 GLU cc_start: 0.8793 (mp0) cc_final: 0.8494 (mp0) REVERT: O 97 ASP cc_start: 0.8429 (t0) cc_final: 0.8147 (t0) REVERT: O 110 PHE cc_start: 0.9245 (t80) cc_final: 0.9035 (t80) REVERT: O 196 MET cc_start: 0.8861 (tpt) cc_final: 0.8506 (tpt) REVERT: O 219 MET cc_start: 0.8685 (ttm) cc_final: 0.8308 (ttm) REVERT: O 254 GLU cc_start: 0.6408 (tt0) cc_final: 0.6178 (tt0) REVERT: O 282 GLU cc_start: 0.7184 (tt0) cc_final: 0.6811 (tt0) REVERT: P 71 PHE cc_start: 0.8521 (p90) cc_final: 0.8235 (p90) REVERT: P 93 ASN cc_start: 0.7996 (t0) cc_final: 0.7696 (t0) REVERT: P 100 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8883 (mp) REVERT: P 112 CYS cc_start: 0.7535 (t) cc_final: 0.7228 (t) REVERT: P 182 ASN cc_start: 0.8400 (m110) cc_final: 0.7686 (m-40) REVERT: P 196 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7034 (mt-10) REVERT: P 300 GLN cc_start: 0.7438 (mt0) cc_final: 0.6984 (mt0) REVERT: P 306 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7602 (tm-30) REVERT: P 329 MET cc_start: 0.8753 (mtp) cc_final: 0.8438 (mtt) REVERT: P 453 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8087 (ttmt) REVERT: Q 34 VAL cc_start: 0.9019 (m) cc_final: 0.8772 (t) REVERT: Q 97 ASP cc_start: 0.8183 (t0) cc_final: 0.7910 (t0) REVERT: Q 107 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8044 (tm-30) REVERT: Q 132 GLN cc_start: 0.8206 (pt0) cc_final: 0.7975 (pt0) REVERT: Q 196 MET cc_start: 0.8767 (tpt) cc_final: 0.8441 (tpt) REVERT: Q 222 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8156 (mp0) REVERT: Q 282 GLU cc_start: 0.7644 (tt0) cc_final: 0.7221 (tt0) REVERT: Q 299 MET cc_start: 0.8393 (ttm) cc_final: 0.8177 (ttp) REVERT: R 117 TYR cc_start: 0.7451 (m-80) cc_final: 0.6530 (m-80) REVERT: R 176 TYR cc_start: 0.8953 (m-10) cc_final: 0.8744 (m-80) REVERT: R 182 ASN cc_start: 0.8465 (m110) cc_final: 0.8096 (m-40) REVERT: R 306 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7438 (tm-30) REVERT: R 453 LYS cc_start: 0.8533 (ttmm) cc_final: 0.7675 (ttmt) REVERT: S 33 ASP cc_start: 0.7737 (t0) cc_final: 0.6923 (t0) REVERT: S 36 GLU cc_start: 0.8950 (mp0) cc_final: 0.7628 (mp0) REVERT: S 97 ASP cc_start: 0.8240 (t0) cc_final: 0.8033 (t0) REVERT: S 149 GLU cc_start: 0.7749 (tt0) cc_final: 0.7547 (tt0) REVERT: S 242 LEU cc_start: 0.9277 (mt) cc_final: 0.8925 (mt) REVERT: S 282 GLU cc_start: 0.7548 (tt0) cc_final: 0.7242 (tt0) REVERT: S 299 MET cc_start: 0.8399 (ttm) cc_final: 0.8192 (ttm) REVERT: T 111 TYR cc_start: 0.8881 (m-80) cc_final: 0.8547 (m-80) REVERT: T 152 ASN cc_start: 0.8236 (m-40) cc_final: 0.7716 (m110) REVERT: T 161 ARG cc_start: 0.7199 (ttp-170) cc_final: 0.6693 (ttp-170) REVERT: T 176 TYR cc_start: 0.8900 (m-10) cc_final: 0.8533 (m-10) REVERT: T 182 ASN cc_start: 0.8411 (m110) cc_final: 0.7725 (m-40) REVERT: T 242 MET cc_start: 0.8894 (tpp) cc_final: 0.8653 (tpt) REVERT: T 306 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8028 (tm-30) REVERT: T 426 TYR cc_start: 0.8330 (m-80) cc_final: 0.8116 (m-80) REVERT: U 36 GLU cc_start: 0.8790 (mp0) cc_final: 0.8495 (mp0) REVERT: U 97 ASP cc_start: 0.8422 (t0) cc_final: 0.8140 (t0) REVERT: U 110 PHE cc_start: 0.9244 (t80) cc_final: 0.9040 (t80) REVERT: U 196 MET cc_start: 0.8846 (tpt) cc_final: 0.8470 (tpt) REVERT: U 219 MET cc_start: 0.8690 (ttm) cc_final: 0.8305 (ttm) REVERT: U 254 GLU cc_start: 0.6410 (tt0) cc_final: 0.6177 (tt0) REVERT: U 282 GLU cc_start: 0.7219 (tt0) cc_final: 0.6843 (tt0) REVERT: V 71 PHE cc_start: 0.8523 (p90) cc_final: 0.8235 (p90) REVERT: V 100 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8877 (mp) REVERT: V 129 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7603 (tpt-90) REVERT: V 182 ASN cc_start: 0.8388 (m110) cc_final: 0.7678 (m-40) REVERT: V 196 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7014 (mt-10) REVERT: V 300 GLN cc_start: 0.7433 (mt0) cc_final: 0.6994 (mt0) REVERT: V 306 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7599 (tm-30) REVERT: V 329 MET cc_start: 0.8722 (mtp) cc_final: 0.8395 (mtt) REVERT: X 34 VAL cc_start: 0.9030 (m) cc_final: 0.8769 (t) REVERT: X 97 ASP cc_start: 0.8198 (t0) cc_final: 0.7921 (t0) REVERT: X 107 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8045 (tm-30) REVERT: X 196 MET cc_start: 0.8758 (tpt) cc_final: 0.8426 (tpt) REVERT: X 222 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8136 (mp0) REVERT: X 282 GLU cc_start: 0.7625 (tt0) cc_final: 0.7219 (tt0) REVERT: X 299 MET cc_start: 0.8368 (ttm) cc_final: 0.8139 (ttp) outliers start: 24 outliers final: 0 residues processed: 1954 average time/residue: 0.6374 time to fit residues: 2100.4408 Evaluate side-chains 1650 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1646 time to evaluate : 5.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 411 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 616 optimal weight: 0.9980 chunk 504 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 742 optimal weight: 0.9980 chunk 801 optimal weight: 0.7980 chunk 661 optimal weight: 0.9990 chunk 736 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 595 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS A 324 GLN A 356 ASN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 ASN B 284 HIS C 106 HIS C 214 ASN D 284 HIS E 214 ASN F 284 HIS F 324 GLN F 356 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN H 284 HIS I 106 HIS ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS K 214 ASN L 284 HIS L 324 GLN L 356 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 ASN N 284 HIS O 106 HIS ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 GLN P 284 HIS Q 214 ASN R 284 HIS R 324 GLN R 356 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN T 55 GLN T 284 HIS U 106 HIS U 214 ASN V 284 HIS ** X 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69108 Z= 0.180 Angle : 0.511 4.750 93204 Z= 0.277 Chirality : 0.042 0.133 9840 Planarity : 0.004 0.035 12240 Dihedral : 4.840 20.535 9120 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.25 % Allowed : 1.86 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.26 (0.09), residues: 8280 helix: 1.05 (0.09), residues: 3120 sheet: -1.43 (0.13), residues: 1260 loop : 0.18 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 146 HIS 0.003 0.001 HIS G 77 PHE 0.022 0.002 PHE S 133 TYR 0.013 0.001 TYR N 422 ARG 0.005 0.001 ARG J 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2206 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2188 time to evaluate : 5.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7718 (tt0) cc_final: 0.7463 (tt0) REVERT: A 78 MET cc_start: 0.6707 (mmp) cc_final: 0.6452 (ptm) REVERT: A 129 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.7170 (tpt-90) REVERT: A 141 GLU cc_start: 0.6369 (pt0) cc_final: 0.6060 (pt0) REVERT: A 158 ASP cc_start: 0.7318 (t70) cc_final: 0.7016 (t70) REVERT: A 182 ASN cc_start: 0.8609 (m110) cc_final: 0.7602 (m-40) REVERT: A 249 THR cc_start: 0.8858 (p) cc_final: 0.8618 (p) REVERT: A 356 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9198 (t0) REVERT: A 411 GLU cc_start: 0.7856 (pp20) cc_final: 0.7653 (pp20) REVERT: A 462 GLN cc_start: 0.7906 (tp40) cc_final: 0.7261 (tt0) REVERT: W 144 ASN cc_start: 0.8449 (p0) cc_final: 0.8189 (p0) REVERT: W 242 LEU cc_start: 0.9296 (mt) cc_final: 0.8975 (mt) REVERT: W 269 MET cc_start: 0.7404 (tmm) cc_final: 0.7161 (tmm) REVERT: W 270 TYR cc_start: 0.7364 (m-80) cc_final: 0.6268 (m-80) REVERT: W 282 GLU cc_start: 0.7327 (tt0) cc_final: 0.7064 (tt0) REVERT: B 141 GLU cc_start: 0.6620 (pt0) cc_final: 0.5964 (pt0) REVERT: B 145 ARG cc_start: 0.8409 (ptp-110) cc_final: 0.7307 (ptp-110) REVERT: B 202 ASP cc_start: 0.8037 (t70) cc_final: 0.7383 (t0) REVERT: B 224 VAL cc_start: 0.9275 (p) cc_final: 0.8950 (t) REVERT: B 244 ILE cc_start: 0.8716 (mm) cc_final: 0.8474 (pt) REVERT: B 306 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7906 (tm-30) REVERT: B 411 GLU cc_start: 0.7932 (pp20) cc_final: 0.7658 (pp20) REVERT: B 453 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7993 (tttm) REVERT: C 107 GLU cc_start: 0.8151 (tp30) cc_final: 0.7927 (tp30) REVERT: C 110 PHE cc_start: 0.9059 (t80) cc_final: 0.8723 (t80) REVERT: C 196 MET cc_start: 0.8629 (tpt) cc_final: 0.8372 (tpt) REVERT: C 217 TRP cc_start: 0.8634 (p90) cc_final: 0.8259 (p90) REVERT: C 219 MET cc_start: 0.8639 (ttm) cc_final: 0.8224 (ttm) REVERT: C 282 GLU cc_start: 0.7117 (tt0) cc_final: 0.6894 (tt0) REVERT: D 129 ARG cc_start: 0.7718 (tpt-90) cc_final: 0.7391 (tpt-90) REVERT: D 141 GLU cc_start: 0.6106 (pt0) cc_final: 0.5609 (pt0) REVERT: D 148 ASP cc_start: 0.8254 (t0) cc_final: 0.7996 (t0) REVERT: D 158 ASP cc_start: 0.7455 (t70) cc_final: 0.7084 (t70) REVERT: D 182 ASN cc_start: 0.8543 (m110) cc_final: 0.7723 (m-40) REVERT: D 196 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6948 (mt-10) REVERT: D 202 ASP cc_start: 0.7816 (t70) cc_final: 0.7436 (t0) REVERT: D 222 ARG cc_start: 0.9269 (ttt90) cc_final: 0.9031 (tpt-90) REVERT: D 236 THR cc_start: 0.8708 (m) cc_final: 0.8497 (p) REVERT: D 239 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6567 (mt-10) REVERT: D 244 ILE cc_start: 0.8845 (mm) cc_final: 0.8604 (pt) REVERT: D 329 MET cc_start: 0.8646 (mtp) cc_final: 0.8312 (mtm) REVERT: D 453 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7025 (tttp) REVERT: E 196 MET cc_start: 0.8574 (tpt) cc_final: 0.8270 (tpt) REVERT: E 282 GLU cc_start: 0.7438 (tt0) cc_final: 0.7089 (tt0) REVERT: F 59 GLU cc_start: 0.7725 (tt0) cc_final: 0.7468 (tt0) REVERT: F 78 MET cc_start: 0.6716 (mmp) cc_final: 0.6452 (ptm) REVERT: F 129 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7177 (tpt-90) REVERT: F 141 GLU cc_start: 0.6367 (pt0) cc_final: 0.6053 (pt0) REVERT: F 158 ASP cc_start: 0.7326 (t70) cc_final: 0.7032 (t70) REVERT: F 182 ASN cc_start: 0.8614 (m110) cc_final: 0.7764 (m-40) REVERT: F 249 THR cc_start: 0.8861 (p) cc_final: 0.8620 (p) REVERT: F 356 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9195 (t0) REVERT: F 411 GLU cc_start: 0.7850 (pp20) cc_final: 0.7585 (pp20) REVERT: G 144 ASN cc_start: 0.8544 (p0) cc_final: 0.8188 (p0) REVERT: G 242 LEU cc_start: 0.9289 (mt) cc_final: 0.8973 (mt) REVERT: G 269 MET cc_start: 0.7360 (tmm) cc_final: 0.7043 (tmm) REVERT: G 270 TYR cc_start: 0.7365 (m-80) cc_final: 0.6270 (m-80) REVERT: G 282 GLU cc_start: 0.7336 (tt0) cc_final: 0.7069 (tt0) REVERT: H 141 GLU cc_start: 0.6624 (pt0) cc_final: 0.5978 (pt0) REVERT: H 145 ARG cc_start: 0.8411 (ptp-110) cc_final: 0.7318 (ptp-110) REVERT: H 202 ASP cc_start: 0.8030 (t70) cc_final: 0.7382 (t0) REVERT: H 224 VAL cc_start: 0.9275 (p) cc_final: 0.8949 (t) REVERT: H 244 ILE cc_start: 0.8717 (mm) cc_final: 0.8470 (pt) REVERT: H 306 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7896 (tm-30) REVERT: H 411 GLU cc_start: 0.7926 (pp20) cc_final: 0.7664 (pp20) REVERT: H 453 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7996 (tttm) REVERT: I 87 GLU cc_start: 0.7638 (tt0) cc_final: 0.7438 (tt0) REVERT: I 107 GLU cc_start: 0.8148 (tp30) cc_final: 0.7946 (tp30) REVERT: I 110 PHE cc_start: 0.9059 (t80) cc_final: 0.8714 (t80) REVERT: I 217 TRP cc_start: 0.8648 (p90) cc_final: 0.8287 (p90) REVERT: I 219 MET cc_start: 0.8629 (ttm) cc_final: 0.8212 (ttm) REVERT: I 282 GLU cc_start: 0.7076 (tt0) cc_final: 0.6821 (tt0) REVERT: J 128 LEU cc_start: 0.8172 (mm) cc_final: 0.7962 (mt) REVERT: J 141 GLU cc_start: 0.6114 (pt0) cc_final: 0.5615 (pt0) REVERT: J 148 ASP cc_start: 0.8248 (t0) cc_final: 0.8001 (t0) REVERT: J 158 ASP cc_start: 0.7457 (t70) cc_final: 0.7082 (t70) REVERT: J 182 ASN cc_start: 0.8529 (m110) cc_final: 0.7706 (m-40) REVERT: J 196 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6949 (mt-10) REVERT: J 202 ASP cc_start: 0.7820 (t70) cc_final: 0.7434 (t0) REVERT: J 222 ARG cc_start: 0.9270 (ttt90) cc_final: 0.9042 (tpt-90) REVERT: J 236 THR cc_start: 0.8713 (m) cc_final: 0.8502 (p) REVERT: J 239 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6582 (mt-10) REVERT: J 244 ILE cc_start: 0.8844 (mm) cc_final: 0.8601 (pt) REVERT: J 329 MET cc_start: 0.8671 (mtp) cc_final: 0.8351 (mtm) REVERT: J 452 PHE cc_start: 0.7168 (t80) cc_final: 0.6855 (t80) REVERT: J 453 LYS cc_start: 0.8164 (ttmm) cc_final: 0.6995 (tttp) REVERT: K 196 MET cc_start: 0.8593 (tpt) cc_final: 0.8284 (tpt) REVERT: K 282 GLU cc_start: 0.7459 (tt0) cc_final: 0.7096 (tt0) REVERT: L 59 GLU cc_start: 0.7730 (tt0) cc_final: 0.7483 (tt0) REVERT: L 78 MET cc_start: 0.6709 (mmp) cc_final: 0.6456 (ptm) REVERT: L 117 TYR cc_start: 0.7853 (m-80) cc_final: 0.7570 (m-80) REVERT: L 129 ARG cc_start: 0.7581 (tpp-160) cc_final: 0.7188 (tpt-90) REVERT: L 158 ASP cc_start: 0.7323 (t70) cc_final: 0.7053 (t70) REVERT: L 182 ASN cc_start: 0.8611 (m110) cc_final: 0.7765 (m-40) REVERT: L 249 THR cc_start: 0.8868 (p) cc_final: 0.8627 (p) REVERT: L 356 ASN cc_start: 0.9468 (OUTLIER) cc_final: 0.9197 (t0) REVERT: M 144 ASN cc_start: 0.8536 (p0) cc_final: 0.8178 (p0) REVERT: M 242 LEU cc_start: 0.9291 (mt) cc_final: 0.8978 (mt) REVERT: M 269 MET cc_start: 0.7360 (tmm) cc_final: 0.7047 (tmm) REVERT: M 270 TYR cc_start: 0.7365 (m-80) cc_final: 0.6270 (m-80) REVERT: M 282 GLU cc_start: 0.7365 (tt0) cc_final: 0.7075 (tt0) REVERT: N 141 GLU cc_start: 0.6621 (pt0) cc_final: 0.5973 (pt0) REVERT: N 145 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.7315 (ptp-110) REVERT: N 202 ASP cc_start: 0.8030 (t70) cc_final: 0.7394 (t0) REVERT: N 224 VAL cc_start: 0.9271 (p) cc_final: 0.8942 (t) REVERT: N 244 ILE cc_start: 0.8720 (mm) cc_final: 0.8473 (pt) REVERT: N 306 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7891 (tm-30) REVERT: N 411 GLU cc_start: 0.7929 (pp20) cc_final: 0.7657 (pp20) REVERT: N 453 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7995 (tttm) REVERT: O 87 GLU cc_start: 0.7654 (tt0) cc_final: 0.7452 (tt0) REVERT: O 107 GLU cc_start: 0.8163 (tp30) cc_final: 0.7954 (tp30) REVERT: O 110 PHE cc_start: 0.9074 (t80) cc_final: 0.8720 (t80) REVERT: O 217 TRP cc_start: 0.8624 (p90) cc_final: 0.8261 (p90) REVERT: O 219 MET cc_start: 0.8631 (ttm) cc_final: 0.8212 (ttm) REVERT: O 282 GLU cc_start: 0.7060 (tt0) cc_final: 0.6823 (tt0) REVERT: P 141 GLU cc_start: 0.6115 (pt0) cc_final: 0.5621 (pt0) REVERT: P 148 ASP cc_start: 0.8248 (t0) cc_final: 0.7992 (t0) REVERT: P 158 ASP cc_start: 0.7458 (t70) cc_final: 0.7081 (t70) REVERT: P 182 ASN cc_start: 0.8524 (m110) cc_final: 0.7709 (m-40) REVERT: P 196 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6949 (mt-10) REVERT: P 202 ASP cc_start: 0.7818 (t70) cc_final: 0.7432 (t0) REVERT: P 222 ARG cc_start: 0.9272 (ttt90) cc_final: 0.9044 (tpt-90) REVERT: P 236 THR cc_start: 0.8718 (m) cc_final: 0.8507 (p) REVERT: P 239 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6579 (mt-10) REVERT: P 244 ILE cc_start: 0.8849 (mm) cc_final: 0.8604 (pt) REVERT: P 329 MET cc_start: 0.8665 (mtp) cc_final: 0.8350 (mtm) REVERT: P 452 PHE cc_start: 0.7163 (t80) cc_final: 0.6841 (t80) REVERT: P 453 LYS cc_start: 0.8165 (ttmm) cc_final: 0.6995 (tttp) REVERT: Q 196 MET cc_start: 0.8579 (tpt) cc_final: 0.8265 (tpt) REVERT: Q 282 GLU cc_start: 0.7452 (tt0) cc_final: 0.7096 (tt0) REVERT: R 59 GLU cc_start: 0.7736 (tt0) cc_final: 0.7479 (tt0) REVERT: R 78 MET cc_start: 0.6707 (mmp) cc_final: 0.6455 (ptm) REVERT: R 117 TYR cc_start: 0.7847 (m-80) cc_final: 0.7567 (m-80) REVERT: R 129 ARG cc_start: 0.7597 (tpp-160) cc_final: 0.7180 (tpt-90) REVERT: R 158 ASP cc_start: 0.7335 (t70) cc_final: 0.7059 (t70) REVERT: R 182 ASN cc_start: 0.8595 (m110) cc_final: 0.7751 (m-40) REVERT: R 236 THR cc_start: 0.8477 (m) cc_final: 0.8186 (p) REVERT: R 239 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6932 (mt-10) REVERT: R 249 THR cc_start: 0.8860 (p) cc_final: 0.8624 (p) REVERT: R 356 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9196 (t0) REVERT: R 411 GLU cc_start: 0.7855 (pp20) cc_final: 0.7586 (pp20) REVERT: S 144 ASN cc_start: 0.8526 (p0) cc_final: 0.8171 (p0) REVERT: S 242 LEU cc_start: 0.9288 (mt) cc_final: 0.8975 (mt) REVERT: S 269 MET cc_start: 0.7404 (tmm) cc_final: 0.7165 (tmm) REVERT: S 270 TYR cc_start: 0.7361 (m-80) cc_final: 0.6267 (m-80) REVERT: S 282 GLU cc_start: 0.7364 (tt0) cc_final: 0.7082 (tt0) REVERT: T 141 GLU cc_start: 0.6618 (pt0) cc_final: 0.5978 (pt0) REVERT: T 145 ARG cc_start: 0.8416 (ptp-110) cc_final: 0.7316 (ptp-110) REVERT: T 202 ASP cc_start: 0.8029 (t70) cc_final: 0.7400 (t0) REVERT: T 224 VAL cc_start: 0.9276 (p) cc_final: 0.8947 (t) REVERT: T 244 ILE cc_start: 0.8714 (mm) cc_final: 0.8465 (pt) REVERT: T 306 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7898 (tm-30) REVERT: T 411 GLU cc_start: 0.7916 (pp20) cc_final: 0.7666 (pp20) REVERT: T 453 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7988 (tttm) REVERT: U 87 GLU cc_start: 0.7633 (tt0) cc_final: 0.7424 (tt0) REVERT: U 107 GLU cc_start: 0.8160 (tp30) cc_final: 0.7939 (tp30) REVERT: U 110 PHE cc_start: 0.9075 (t80) cc_final: 0.8725 (t80) REVERT: U 217 TRP cc_start: 0.8629 (p90) cc_final: 0.8258 (p90) REVERT: U 219 MET cc_start: 0.8634 (ttm) cc_final: 0.8208 (ttm) REVERT: U 242 LEU cc_start: 0.9213 (mt) cc_final: 0.8997 (mt) REVERT: U 282 GLU cc_start: 0.7099 (tt0) cc_final: 0.6896 (tt0) REVERT: V 129 ARG cc_start: 0.7737 (tpt-90) cc_final: 0.7426 (tpt-90) REVERT: V 141 GLU cc_start: 0.6119 (pt0) cc_final: 0.5629 (pt0) REVERT: V 148 ASP cc_start: 0.8269 (t0) cc_final: 0.8015 (t0) REVERT: V 158 ASP cc_start: 0.7457 (t70) cc_final: 0.7086 (t70) REVERT: V 182 ASN cc_start: 0.8520 (m110) cc_final: 0.7681 (m-40) REVERT: V 196 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6947 (mt-10) REVERT: V 202 ASP cc_start: 0.7822 (t70) cc_final: 0.7435 (t0) REVERT: V 222 ARG cc_start: 0.9284 (ttt90) cc_final: 0.9042 (tpt-90) REVERT: V 236 THR cc_start: 0.8717 (m) cc_final: 0.8501 (p) REVERT: V 239 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6583 (mt-10) REVERT: V 244 ILE cc_start: 0.8853 (mm) cc_final: 0.8603 (pt) REVERT: V 329 MET cc_start: 0.8637 (mtp) cc_final: 0.8299 (mtm) REVERT: V 452 PHE cc_start: 0.7318 (t80) cc_final: 0.6553 (t80) REVERT: V 453 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7015 (tttp) REVERT: X 196 MET cc_start: 0.8559 (tpt) cc_final: 0.8245 (tpt) REVERT: X 282 GLU cc_start: 0.7422 (tt0) cc_final: 0.7077 (tt0) REVERT: X 299 MET cc_start: 0.8148 (ttm) cc_final: 0.7901 (ttp) outliers start: 18 outliers final: 0 residues processed: 2202 average time/residue: 0.6756 time to fit residues: 2511.3848 Evaluate side-chains 1677 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1673 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 733 optimal weight: 0.9980 chunk 558 optimal weight: 6.9990 chunk 385 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 354 optimal weight: 6.9990 chunk 498 optimal weight: 3.9990 chunk 745 optimal weight: 8.9990 chunk 788 optimal weight: 0.4980 chunk 389 optimal weight: 1.9990 chunk 706 optimal weight: 1.9990 chunk 212 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 ASN C 39 ASN C 214 ASN D 284 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 214 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN I 39 ASN I 214 ASN J 284 HIS ** J 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 214 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 ASN O 39 ASN ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 284 HIS ** P 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 ASN Q 214 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN U 39 ASN U 214 ASN V 54 GLN V 284 HIS ** V 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN X 214 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 69108 Z= 0.159 Angle : 0.497 10.463 93204 Z= 0.266 Chirality : 0.041 0.135 9840 Planarity : 0.004 0.041 12240 Dihedral : 4.530 18.928 9120 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.15 % Allowed : 2.06 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.42 (0.09), residues: 8280 helix: 1.13 (0.09), residues: 3204 sheet: -1.29 (0.14), residues: 1236 loop : 0.26 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 146 HIS 0.006 0.001 HIS G 77 PHE 0.020 0.001 PHE C 133 TYR 0.010 0.001 TYR C 294 ARG 0.008 0.001 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2160 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2149 time to evaluate : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6779 (mmp) cc_final: 0.6471 (ptm) REVERT: A 100 ILE cc_start: 0.8889 (mp) cc_final: 0.8616 (mp) REVERT: A 161 ARG cc_start: 0.7381 (ttp80) cc_final: 0.6731 (ttp-170) REVERT: A 182 ASN cc_start: 0.8642 (m110) cc_final: 0.7166 (m-40) REVERT: A 239 GLU cc_start: 0.6716 (tt0) cc_final: 0.6335 (tt0) REVERT: A 242 MET cc_start: 0.8894 (tpt) cc_final: 0.8214 (tpt) REVERT: A 249 THR cc_start: 0.8867 (p) cc_final: 0.8582 (p) REVERT: A 253 SER cc_start: 0.8004 (m) cc_final: 0.7762 (p) REVERT: A 411 GLU cc_start: 0.7860 (pp20) cc_final: 0.7530 (pp20) REVERT: A 428 PHE cc_start: 0.8729 (t80) cc_final: 0.8424 (t80) REVERT: A 453 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7595 (ttmm) REVERT: A 462 GLN cc_start: 0.7683 (tp40) cc_final: 0.7093 (tt0) REVERT: W 144 ASN cc_start: 0.8406 (p0) cc_final: 0.8070 (p0) REVERT: W 242 LEU cc_start: 0.9219 (mt) cc_final: 0.9009 (mt) REVERT: W 270 TYR cc_start: 0.7208 (m-80) cc_final: 0.6105 (m-80) REVERT: W 282 GLU cc_start: 0.7266 (tt0) cc_final: 0.7021 (tt0) REVERT: B 112 CYS cc_start: 0.7482 (t) cc_final: 0.7190 (t) REVERT: B 129 ARG cc_start: 0.7434 (tpp-160) cc_final: 0.7081 (tpt-90) REVERT: B 141 GLU cc_start: 0.6532 (pt0) cc_final: 0.5744 (pt0) REVERT: B 145 ARG cc_start: 0.8314 (ptp-110) cc_final: 0.7346 (ptp-110) REVERT: B 202 ASP cc_start: 0.8040 (t70) cc_final: 0.7417 (t0) REVERT: B 224 VAL cc_start: 0.9293 (p) cc_final: 0.8986 (t) REVERT: B 236 THR cc_start: 0.8524 (m) cc_final: 0.8277 (p) REVERT: B 239 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6709 (mt-10) REVERT: B 244 ILE cc_start: 0.8709 (mm) cc_final: 0.8504 (pt) REVERT: B 249 THR cc_start: 0.8617 (p) cc_final: 0.8396 (p) REVERT: B 306 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7811 (tm-30) REVERT: C 91 ASP cc_start: 0.6438 (t0) cc_final: 0.6234 (t70) REVERT: C 196 MET cc_start: 0.8713 (tpt) cc_final: 0.8483 (tpt) REVERT: C 217 TRP cc_start: 0.8639 (p90) cc_final: 0.8259 (p90) REVERT: C 234 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7381 (mm-30) REVERT: C 282 GLU cc_start: 0.6992 (tt0) cc_final: 0.6738 (tt0) REVERT: D 78 MET cc_start: 0.6840 (mmm) cc_final: 0.6623 (ptm) REVERT: D 100 ILE cc_start: 0.8979 (mp) cc_final: 0.8775 (mp) REVERT: D 117 TYR cc_start: 0.7686 (m-80) cc_final: 0.6941 (m-80) REVERT: D 158 ASP cc_start: 0.7407 (t70) cc_final: 0.7079 (t70) REVERT: D 182 ASN cc_start: 0.8586 (m110) cc_final: 0.7583 (m-40) REVERT: D 196 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6786 (mt-10) REVERT: D 202 ASP cc_start: 0.7827 (t70) cc_final: 0.7115 (t0) REVERT: D 239 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6616 (mt-10) REVERT: D 244 ILE cc_start: 0.8741 (mm) cc_final: 0.8521 (pt) REVERT: D 329 MET cc_start: 0.8635 (mtp) cc_final: 0.8387 (mtt) REVERT: D 359 SER cc_start: 0.9175 (m) cc_final: 0.8971 (m) REVERT: D 452 PHE cc_start: 0.7032 (t80) cc_final: 0.6761 (t80) REVERT: D 453 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6770 (tttp) REVERT: E 36 GLU cc_start: 0.8732 (mp0) cc_final: 0.8384 (mp0) REVERT: E 107 GLU cc_start: 0.8126 (tp30) cc_final: 0.7903 (tp30) REVERT: E 146 TRP cc_start: 0.9129 (p90) cc_final: 0.8828 (p90) REVERT: E 217 TRP cc_start: 0.8950 (p90) cc_final: 0.8418 (p90) REVERT: E 282 GLU cc_start: 0.7425 (tt0) cc_final: 0.7109 (tt0) REVERT: F 78 MET cc_start: 0.6781 (mmp) cc_final: 0.6469 (ptm) REVERT: F 100 ILE cc_start: 0.8888 (mp) cc_final: 0.8616 (mp) REVERT: F 161 ARG cc_start: 0.7405 (ttp80) cc_final: 0.6735 (ttp-170) REVERT: F 182 ASN cc_start: 0.8620 (m110) cc_final: 0.7456 (m-40) REVERT: F 239 GLU cc_start: 0.6649 (tt0) cc_final: 0.6307 (tt0) REVERT: F 240 LEU cc_start: 0.8777 (tt) cc_final: 0.8501 (tt) REVERT: F 242 MET cc_start: 0.8787 (tpt) cc_final: 0.8528 (tpt) REVERT: F 249 THR cc_start: 0.8870 (p) cc_final: 0.8582 (p) REVERT: F 253 SER cc_start: 0.8002 (m) cc_final: 0.7772 (p) REVERT: F 411 GLU cc_start: 0.7834 (pp20) cc_final: 0.7507 (pp20) REVERT: F 428 PHE cc_start: 0.8724 (t80) cc_final: 0.8444 (t80) REVERT: F 453 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7600 (ttmm) REVERT: F 462 GLN cc_start: 0.7859 (tp40) cc_final: 0.6934 (tt0) REVERT: G 144 ASN cc_start: 0.8365 (p0) cc_final: 0.8086 (p0) REVERT: G 242 LEU cc_start: 0.9217 (mt) cc_final: 0.9002 (mt) REVERT: G 270 TYR cc_start: 0.7203 (m-80) cc_final: 0.6109 (m-80) REVERT: G 282 GLU cc_start: 0.7262 (tt0) cc_final: 0.7026 (tt0) REVERT: H 112 CYS cc_start: 0.7484 (t) cc_final: 0.7193 (t) REVERT: H 129 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7076 (tpt-90) REVERT: H 141 GLU cc_start: 0.6535 (pt0) cc_final: 0.5748 (pt0) REVERT: H 145 ARG cc_start: 0.8311 (ptp-110) cc_final: 0.7347 (ptp-110) REVERT: H 202 ASP cc_start: 0.8041 (t70) cc_final: 0.7415 (t0) REVERT: H 224 VAL cc_start: 0.9297 (p) cc_final: 0.8983 (t) REVERT: H 249 THR cc_start: 0.8627 (p) cc_final: 0.8397 (p) REVERT: H 306 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7798 (tm-30) REVERT: I 91 ASP cc_start: 0.6445 (t0) cc_final: 0.6235 (t70) REVERT: I 217 TRP cc_start: 0.8677 (p90) cc_final: 0.8310 (p90) REVERT: I 234 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7394 (mm-30) REVERT: I 282 GLU cc_start: 0.6960 (tt0) cc_final: 0.6740 (tt0) REVERT: J 78 MET cc_start: 0.6822 (mmm) cc_final: 0.6616 (ptm) REVERT: J 100 ILE cc_start: 0.8983 (mp) cc_final: 0.8771 (mp) REVERT: J 117 TYR cc_start: 0.7668 (m-80) cc_final: 0.6935 (m-80) REVERT: J 128 LEU cc_start: 0.8030 (mm) cc_final: 0.7684 (tp) REVERT: J 158 ASP cc_start: 0.7411 (t70) cc_final: 0.7081 (t70) REVERT: J 182 ASN cc_start: 0.8609 (m110) cc_final: 0.7599 (m-40) REVERT: J 196 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6778 (mt-10) REVERT: J 202 ASP cc_start: 0.7810 (t70) cc_final: 0.7111 (t0) REVERT: J 239 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6636 (mt-10) REVERT: J 244 ILE cc_start: 0.8737 (mm) cc_final: 0.8523 (pt) REVERT: J 329 MET cc_start: 0.8656 (mtp) cc_final: 0.8427 (mtt) REVERT: J 359 SER cc_start: 0.9178 (m) cc_final: 0.8967 (m) REVERT: J 453 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7087 (tttp) REVERT: K 36 GLU cc_start: 0.8739 (mp0) cc_final: 0.8404 (mp0) REVERT: K 107 GLU cc_start: 0.8128 (tp30) cc_final: 0.7903 (tp30) REVERT: K 146 TRP cc_start: 0.9127 (p90) cc_final: 0.8829 (p90) REVERT: K 217 TRP cc_start: 0.8944 (p90) cc_final: 0.8419 (p90) REVERT: K 282 GLU cc_start: 0.7439 (tt0) cc_final: 0.7112 (tt0) REVERT: L 78 MET cc_start: 0.6770 (mmp) cc_final: 0.6469 (ptm) REVERT: L 100 ILE cc_start: 0.8877 (mp) cc_final: 0.8606 (mp) REVERT: L 112 CYS cc_start: 0.7359 (t) cc_final: 0.7154 (t) REVERT: L 144 LYS cc_start: 0.8161 (mttt) cc_final: 0.7894 (mtmt) REVERT: L 145 ARG cc_start: 0.8292 (ptp90) cc_final: 0.8039 (ttm110) REVERT: L 161 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6719 (ttp-170) REVERT: L 182 ASN cc_start: 0.8628 (m110) cc_final: 0.7454 (m-40) REVERT: L 239 GLU cc_start: 0.6656 (tt0) cc_final: 0.6314 (tt0) REVERT: L 240 LEU cc_start: 0.8776 (tt) cc_final: 0.8505 (tt) REVERT: L 242 MET cc_start: 0.8787 (tpt) cc_final: 0.8530 (tpt) REVERT: L 249 THR cc_start: 0.8880 (p) cc_final: 0.8582 (p) REVERT: L 411 GLU cc_start: 0.7816 (pp20) cc_final: 0.7548 (pp20) REVERT: L 428 PHE cc_start: 0.8736 (t80) cc_final: 0.8467 (t80) REVERT: L 453 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7601 (ttmm) REVERT: M 144 ASN cc_start: 0.8354 (p0) cc_final: 0.8073 (p0) REVERT: M 242 LEU cc_start: 0.9217 (mt) cc_final: 0.9014 (mt) REVERT: M 270 TYR cc_start: 0.7205 (m-80) cc_final: 0.6108 (m-80) REVERT: M 282 GLU cc_start: 0.7301 (tt0) cc_final: 0.7044 (tt0) REVERT: N 112 CYS cc_start: 0.7483 (t) cc_final: 0.7192 (t) REVERT: N 129 ARG cc_start: 0.7434 (tpp-160) cc_final: 0.7074 (tpt-90) REVERT: N 141 GLU cc_start: 0.6532 (pt0) cc_final: 0.5758 (pt0) REVERT: N 145 ARG cc_start: 0.8322 (ptp-110) cc_final: 0.7360 (ptp-110) REVERT: N 202 ASP cc_start: 0.8041 (t70) cc_final: 0.7414 (t0) REVERT: N 224 VAL cc_start: 0.9293 (p) cc_final: 0.8980 (t) REVERT: N 244 ILE cc_start: 0.8708 (mm) cc_final: 0.8508 (pt) REVERT: N 249 THR cc_start: 0.8623 (p) cc_final: 0.8396 (p) REVERT: N 306 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7791 (tm-30) REVERT: O 217 TRP cc_start: 0.8636 (p90) cc_final: 0.8270 (p90) REVERT: O 234 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7404 (mm-30) REVERT: O 282 GLU cc_start: 0.6946 (tt0) cc_final: 0.6743 (tt0) REVERT: P 78 MET cc_start: 0.6834 (mmm) cc_final: 0.6607 (ptm) REVERT: P 100 ILE cc_start: 0.8980 (mp) cc_final: 0.8772 (mp) REVERT: P 117 TYR cc_start: 0.7670 (m-80) cc_final: 0.6920 (m-80) REVERT: P 158 ASP cc_start: 0.7409 (t70) cc_final: 0.7085 (t70) REVERT: P 182 ASN cc_start: 0.8609 (m110) cc_final: 0.7599 (m-40) REVERT: P 196 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6778 (mt-10) REVERT: P 202 ASP cc_start: 0.7815 (t70) cc_final: 0.7112 (t0) REVERT: P 239 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6630 (mt-10) REVERT: P 244 ILE cc_start: 0.8743 (mm) cc_final: 0.8518 (pt) REVERT: P 329 MET cc_start: 0.8643 (mtp) cc_final: 0.8418 (mtt) REVERT: P 359 SER cc_start: 0.9179 (m) cc_final: 0.8964 (m) REVERT: P 453 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7100 (tttp) REVERT: Q 36 GLU cc_start: 0.8729 (mp0) cc_final: 0.8387 (mp0) REVERT: Q 107 GLU cc_start: 0.8136 (tp30) cc_final: 0.7921 (tp30) REVERT: Q 146 TRP cc_start: 0.9131 (p90) cc_final: 0.8833 (p90) REVERT: Q 217 TRP cc_start: 0.8932 (p90) cc_final: 0.8377 (p90) REVERT: Q 222 GLU cc_start: 0.8286 (mp0) cc_final: 0.8052 (mp0) REVERT: Q 282 GLU cc_start: 0.7431 (tt0) cc_final: 0.7137 (tt0) REVERT: R 78 MET cc_start: 0.6776 (mmp) cc_final: 0.6470 (ptm) REVERT: R 100 ILE cc_start: 0.8877 (mp) cc_final: 0.8601 (mp) REVERT: R 112 CYS cc_start: 0.7366 (t) cc_final: 0.7158 (t) REVERT: R 144 LYS cc_start: 0.8243 (mttt) cc_final: 0.8016 (mtmt) REVERT: R 145 ARG cc_start: 0.8322 (ptp90) cc_final: 0.8011 (ttm110) REVERT: R 161 ARG cc_start: 0.7370 (ttp80) cc_final: 0.6713 (ttp-170) REVERT: R 182 ASN cc_start: 0.8660 (m110) cc_final: 0.7484 (m-40) REVERT: R 239 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6430 (mt-10) REVERT: R 240 LEU cc_start: 0.8828 (tt) cc_final: 0.8417 (tt) REVERT: R 242 MET cc_start: 0.8775 (tpt) cc_final: 0.8538 (tpt) REVERT: R 249 THR cc_start: 0.8867 (p) cc_final: 0.8577 (p) REVERT: R 253 SER cc_start: 0.7998 (m) cc_final: 0.7792 (p) REVERT: R 411 GLU cc_start: 0.7836 (pp20) cc_final: 0.7534 (pp20) REVERT: R 428 PHE cc_start: 0.8712 (t80) cc_final: 0.8436 (t80) REVERT: R 452 PHE cc_start: 0.6817 (t80) cc_final: 0.6616 (t80) REVERT: R 453 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7603 (ttmm) REVERT: S 144 ASN cc_start: 0.8362 (p0) cc_final: 0.8055 (p0) REVERT: S 242 LEU cc_start: 0.9214 (mt) cc_final: 0.9011 (mt) REVERT: S 270 TYR cc_start: 0.7198 (m-80) cc_final: 0.6106 (m-80) REVERT: S 282 GLU cc_start: 0.7304 (tt0) cc_final: 0.7038 (tt0) REVERT: T 112 CYS cc_start: 0.7495 (t) cc_final: 0.7195 (t) REVERT: T 129 ARG cc_start: 0.7433 (tpp-160) cc_final: 0.7065 (tpt-90) REVERT: T 141 GLU cc_start: 0.6531 (pt0) cc_final: 0.5755 (pt0) REVERT: T 145 ARG cc_start: 0.8307 (ptp-110) cc_final: 0.7348 (ptp-110) REVERT: T 202 ASP cc_start: 0.8051 (t70) cc_final: 0.7418 (t0) REVERT: T 224 VAL cc_start: 0.9297 (p) cc_final: 0.8984 (t) REVERT: T 244 ILE cc_start: 0.8710 (mm) cc_final: 0.8508 (pt) REVERT: T 249 THR cc_start: 0.8616 (p) cc_final: 0.8388 (p) REVERT: T 306 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7795 (tm-30) REVERT: U 217 TRP cc_start: 0.8637 (p90) cc_final: 0.8262 (p90) REVERT: U 282 GLU cc_start: 0.6969 (tt0) cc_final: 0.6749 (tt0) REVERT: V 78 MET cc_start: 0.6835 (mmm) cc_final: 0.6624 (ptm) REVERT: V 100 ILE cc_start: 0.8981 (mp) cc_final: 0.8775 (mp) REVERT: V 117 TYR cc_start: 0.7630 (m-80) cc_final: 0.6878 (m-80) REVERT: V 129 ARG cc_start: 0.7576 (tpt-90) cc_final: 0.7360 (tpt-90) REVERT: V 158 ASP cc_start: 0.7409 (t70) cc_final: 0.7090 (t70) REVERT: V 182 ASN cc_start: 0.8591 (m110) cc_final: 0.7595 (m-40) REVERT: V 196 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6783 (mt-10) REVERT: V 202 ASP cc_start: 0.7820 (t70) cc_final: 0.7109 (t0) REVERT: V 239 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6625 (mt-10) REVERT: V 244 ILE cc_start: 0.8746 (mm) cc_final: 0.8522 (pt) REVERT: V 329 MET cc_start: 0.8617 (mtp) cc_final: 0.8376 (mtt) REVERT: V 359 SER cc_start: 0.9175 (m) cc_final: 0.8974 (m) REVERT: V 452 PHE cc_start: 0.7287 (t80) cc_final: 0.6447 (t80) REVERT: V 453 LYS cc_start: 0.7449 (ttmt) cc_final: 0.6791 (tttp) REVERT: X 36 GLU cc_start: 0.8737 (mp0) cc_final: 0.8397 (mp0) REVERT: X 107 GLU cc_start: 0.8140 (tp30) cc_final: 0.7903 (tp30) REVERT: X 146 TRP cc_start: 0.9134 (p90) cc_final: 0.8832 (p90) REVERT: X 217 TRP cc_start: 0.8951 (p90) cc_final: 0.8391 (p90) REVERT: X 222 GLU cc_start: 0.8266 (mp0) cc_final: 0.8031 (mp0) REVERT: X 282 GLU cc_start: 0.7412 (tt0) cc_final: 0.7111 (tt0) outliers start: 11 outliers final: 0 residues processed: 2160 average time/residue: 0.6522 time to fit residues: 2392.2885 Evaluate side-chains 1763 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1763 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 656 optimal weight: 3.9990 chunk 447 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 587 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 673 optimal weight: 3.9990 chunk 545 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 402 optimal weight: 2.9990 chunk 707 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 356 ASN W 77 HIS ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 214 ASN F 54 GLN F 113 GLN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN F 324 GLN F 356 ASN G 77 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 HIS K 214 ASN L 54 GLN L 113 GLN ** L 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 GLN L 356 ASN M 77 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 ASN ** N 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 GLN ** P 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 HIS ** Q 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 GLN R 356 ASN S 77 HIS ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN ** T 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 180 GLN ** V 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 HIS ** X 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 69108 Z= 0.449 Angle : 0.681 12.128 93204 Z= 0.362 Chirality : 0.047 0.159 9840 Planarity : 0.005 0.145 12240 Dihedral : 5.169 20.846 9120 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.04 (0.09), residues: 8280 helix: 0.69 (0.09), residues: 3168 sheet: -1.35 (0.14), residues: 1236 loop : -0.01 (0.10), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 312 HIS 0.006 0.002 HIS B 303 PHE 0.022 0.002 PHE F 452 TYR 0.022 0.002 TYR T 422 ARG 0.016 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2024 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2014 time to evaluate : 5.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9008 (mp) cc_final: 0.8786 (mp) REVERT: A 112 CYS cc_start: 0.7374 (t) cc_final: 0.7121 (t) REVERT: A 158 ASP cc_start: 0.7465 (t70) cc_final: 0.7109 (t70) REVERT: A 176 TYR cc_start: 0.8836 (m-10) cc_final: 0.8445 (m-10) REVERT: A 182 ASN cc_start: 0.8556 (m110) cc_final: 0.8210 (m-40) REVERT: A 306 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7486 (tm-30) REVERT: A 356 ASN cc_start: 0.9475 (OUTLIER) cc_final: 0.9198 (t0) REVERT: A 411 GLU cc_start: 0.8070 (pp20) cc_final: 0.7687 (pp20) REVERT: A 428 PHE cc_start: 0.8855 (t80) cc_final: 0.8596 (t80) REVERT: A 448 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8029 (tp30) REVERT: A 453 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7865 (ttmm) REVERT: W 33 ASP cc_start: 0.7720 (t0) cc_final: 0.7247 (t70) REVERT: W 36 GLU cc_start: 0.8817 (mp0) cc_final: 0.7862 (mp0) REVERT: W 144 ASN cc_start: 0.8540 (p0) cc_final: 0.8206 (p0) REVERT: W 242 LEU cc_start: 0.9242 (mt) cc_final: 0.8938 (mt) REVERT: W 282 GLU cc_start: 0.7363 (tt0) cc_final: 0.7065 (tt0) REVERT: W 299 MET cc_start: 0.8326 (ttm) cc_final: 0.8122 (ttp) REVERT: B 112 CYS cc_start: 0.7625 (t) cc_final: 0.6716 (t) REVERT: B 117 TYR cc_start: 0.7644 (m-80) cc_final: 0.7254 (m-80) REVERT: B 129 ARG cc_start: 0.7670 (tpp-160) cc_final: 0.7307 (tpt-90) REVERT: B 145 ARG cc_start: 0.8459 (ptp-110) cc_final: 0.7103 (ptp-110) REVERT: B 182 ASN cc_start: 0.8565 (m110) cc_final: 0.8037 (m110) REVERT: B 244 ILE cc_start: 0.8831 (mm) cc_final: 0.8544 (pt) REVERT: B 306 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7985 (tm-30) REVERT: B 453 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7797 (ttmm) REVERT: C 33 ASP cc_start: 0.7801 (t0) cc_final: 0.7184 (t70) REVERT: C 35 SER cc_start: 0.8760 (t) cc_final: 0.8326 (t) REVERT: C 36 GLU cc_start: 0.8760 (mp0) cc_final: 0.7423 (mp0) REVERT: C 219 MET cc_start: 0.8673 (ttm) cc_final: 0.8333 (ttm) REVERT: D 100 ILE cc_start: 0.9039 (mp) cc_final: 0.8749 (mp) REVERT: D 112 CYS cc_start: 0.7371 (t) cc_final: 0.7162 (t) REVERT: D 158 ASP cc_start: 0.7529 (t70) cc_final: 0.7134 (t70) REVERT: D 182 ASN cc_start: 0.8630 (m110) cc_final: 0.7565 (m-40) REVERT: D 196 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6665 (mt-10) REVERT: D 242 MET cc_start: 0.8852 (tpt) cc_final: 0.8322 (tpt) REVERT: D 306 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7729 (tm-30) REVERT: D 329 MET cc_start: 0.8712 (mtp) cc_final: 0.8415 (mtt) REVERT: D 448 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7636 (tp30) REVERT: D 453 LYS cc_start: 0.7563 (ttmt) cc_final: 0.6829 (tttp) REVERT: E 269 MET cc_start: 0.8120 (ptt) cc_final: 0.7747 (tmm) REVERT: E 282 GLU cc_start: 0.7502 (tt0) cc_final: 0.7153 (tt0) REVERT: F 100 ILE cc_start: 0.9010 (mp) cc_final: 0.8792 (mp) REVERT: F 112 CYS cc_start: 0.7375 (t) cc_final: 0.7089 (t) REVERT: F 158 ASP cc_start: 0.7477 (t70) cc_final: 0.7137 (t70) REVERT: F 176 TYR cc_start: 0.8824 (m-10) cc_final: 0.8440 (m-10) REVERT: F 182 ASN cc_start: 0.8601 (m110) cc_final: 0.8086 (m-40) REVERT: F 196 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7143 (mt-10) REVERT: F 306 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7415 (tm-30) REVERT: F 356 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.9201 (t0) REVERT: F 411 GLU cc_start: 0.8061 (pp20) cc_final: 0.7756 (pp20) REVERT: F 448 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8010 (tp30) REVERT: F 453 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7894 (ttmm) REVERT: G 36 GLU cc_start: 0.8821 (mp0) cc_final: 0.8596 (mp0) REVERT: G 144 ASN cc_start: 0.8528 (p0) cc_final: 0.8205 (p0) REVERT: G 242 LEU cc_start: 0.9244 (mt) cc_final: 0.8914 (mt) REVERT: G 282 GLU cc_start: 0.7368 (tt0) cc_final: 0.7070 (tt0) REVERT: G 299 MET cc_start: 0.8372 (ttm) cc_final: 0.8081 (ttp) REVERT: H 112 CYS cc_start: 0.7727 (t) cc_final: 0.6831 (t) REVERT: H 113 GLN cc_start: 0.7199 (mm110) cc_final: 0.6978 (mm110) REVERT: H 129 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.7315 (tpt-90) REVERT: H 145 ARG cc_start: 0.8458 (ptp-110) cc_final: 0.7106 (ptp-110) REVERT: H 182 ASN cc_start: 0.8539 (m110) cc_final: 0.8010 (m110) REVERT: H 306 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7926 (tm-30) REVERT: H 453 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7781 (ttmm) REVERT: I 33 ASP cc_start: 0.7840 (t0) cc_final: 0.7343 (t70) REVERT: I 35 SER cc_start: 0.8801 (t) cc_final: 0.8531 (t) REVERT: I 36 GLU cc_start: 0.8806 (mp0) cc_final: 0.7936 (mp0) REVERT: I 219 MET cc_start: 0.8672 (ttm) cc_final: 0.8334 (ttm) REVERT: I 282 GLU cc_start: 0.7080 (tt0) cc_final: 0.6726 (tt0) REVERT: J 100 ILE cc_start: 0.9041 (mp) cc_final: 0.8743 (mp) REVERT: J 112 CYS cc_start: 0.7370 (t) cc_final: 0.7166 (t) REVERT: J 158 ASP cc_start: 0.7505 (t70) cc_final: 0.7128 (t70) REVERT: J 182 ASN cc_start: 0.8620 (m110) cc_final: 0.7565 (m-40) REVERT: J 196 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6666 (mt-10) REVERT: J 202 ASP cc_start: 0.7947 (t70) cc_final: 0.7741 (t0) REVERT: J 242 MET cc_start: 0.8858 (tpt) cc_final: 0.8320 (tpt) REVERT: J 306 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7723 (tm-30) REVERT: J 329 MET cc_start: 0.8669 (mtp) cc_final: 0.8322 (mtt) REVERT: J 448 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7948 (tp30) REVERT: J 453 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7191 (tttp) REVERT: K 254 GLU cc_start: 0.6900 (tt0) cc_final: 0.6700 (tt0) REVERT: K 269 MET cc_start: 0.8111 (ptt) cc_final: 0.7742 (tmm) REVERT: K 282 GLU cc_start: 0.7512 (tt0) cc_final: 0.7151 (tt0) REVERT: L 100 ILE cc_start: 0.8998 (mp) cc_final: 0.8766 (mp) REVERT: L 112 CYS cc_start: 0.7704 (t) cc_final: 0.6893 (t) REVERT: L 113 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7229 (mm110) REVERT: L 145 ARG cc_start: 0.8464 (ptp90) cc_final: 0.8112 (ttm110) REVERT: L 158 ASP cc_start: 0.7476 (t70) cc_final: 0.7131 (t70) REVERT: L 176 TYR cc_start: 0.8830 (m-10) cc_final: 0.8526 (m-10) REVERT: L 182 ASN cc_start: 0.8585 (m110) cc_final: 0.8051 (m-40) REVERT: L 196 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7192 (mt-10) REVERT: L 306 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7450 (tm-30) REVERT: L 356 ASN cc_start: 0.9481 (OUTLIER) cc_final: 0.9201 (t0) REVERT: L 411 GLU cc_start: 0.8075 (pp20) cc_final: 0.7704 (pp20) REVERT: L 448 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8026 (tp30) REVERT: L 453 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7891 (ttmm) REVERT: M 36 GLU cc_start: 0.8825 (mp0) cc_final: 0.8616 (mp0) REVERT: M 144 ASN cc_start: 0.8522 (p0) cc_final: 0.8197 (p0) REVERT: M 242 LEU cc_start: 0.9243 (mt) cc_final: 0.8913 (mt) REVERT: M 282 GLU cc_start: 0.7418 (tt0) cc_final: 0.7093 (tt0) REVERT: M 299 MET cc_start: 0.8360 (ttm) cc_final: 0.8092 (ttp) REVERT: N 112 CYS cc_start: 0.7724 (t) cc_final: 0.6851 (t) REVERT: N 117 TYR cc_start: 0.7594 (m-80) cc_final: 0.7383 (m-80) REVERT: N 129 ARG cc_start: 0.7660 (tpp-160) cc_final: 0.7303 (tpt-90) REVERT: N 145 ARG cc_start: 0.8476 (ptp-110) cc_final: 0.7100 (ptp-110) REVERT: N 182 ASN cc_start: 0.8548 (m110) cc_final: 0.7982 (m110) REVERT: N 244 ILE cc_start: 0.8835 (mm) cc_final: 0.8560 (pt) REVERT: N 306 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7934 (tm-30) REVERT: N 453 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7787 (ttmm) REVERT: O 33 ASP cc_start: 0.7802 (t0) cc_final: 0.7170 (t70) REVERT: O 35 SER cc_start: 0.8772 (t) cc_final: 0.8341 (t) REVERT: O 36 GLU cc_start: 0.8759 (mp0) cc_final: 0.7426 (mp0) REVERT: O 219 MET cc_start: 0.8686 (ttm) cc_final: 0.8362 (ttm) REVERT: O 282 GLU cc_start: 0.7075 (tt0) cc_final: 0.6733 (tt0) REVERT: P 100 ILE cc_start: 0.9042 (mp) cc_final: 0.8751 (mp) REVERT: P 158 ASP cc_start: 0.7466 (t70) cc_final: 0.7082 (t70) REVERT: P 182 ASN cc_start: 0.8638 (m110) cc_final: 0.7578 (m-40) REVERT: P 196 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6677 (mt-10) REVERT: P 202 ASP cc_start: 0.7943 (t70) cc_final: 0.7736 (t0) REVERT: P 242 MET cc_start: 0.8859 (tpt) cc_final: 0.8316 (tpt) REVERT: P 306 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7721 (tm-30) REVERT: P 329 MET cc_start: 0.8656 (mtp) cc_final: 0.8316 (mtt) REVERT: P 448 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7947 (tp30) REVERT: P 453 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7202 (tttp) REVERT: Q 254 GLU cc_start: 0.6909 (tt0) cc_final: 0.6704 (tt0) REVERT: Q 269 MET cc_start: 0.8112 (ptt) cc_final: 0.7741 (tmm) REVERT: Q 282 GLU cc_start: 0.7549 (tt0) cc_final: 0.7176 (tt0) REVERT: R 100 ILE cc_start: 0.8997 (mp) cc_final: 0.8786 (mp) REVERT: R 112 CYS cc_start: 0.7712 (t) cc_final: 0.6889 (t) REVERT: R 113 GLN cc_start: 0.7362 (mm110) cc_final: 0.7081 (mm110) REVERT: R 145 ARG cc_start: 0.8427 (ptp90) cc_final: 0.8109 (ttm110) REVERT: R 158 ASP cc_start: 0.7500 (t70) cc_final: 0.7152 (t70) REVERT: R 176 TYR cc_start: 0.8833 (m-10) cc_final: 0.8446 (m-10) REVERT: R 182 ASN cc_start: 0.8581 (m110) cc_final: 0.7227 (m-40) REVERT: R 242 MET cc_start: 0.9038 (tpt) cc_final: 0.8222 (tpt) REVERT: R 306 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7453 (tm-30) REVERT: R 356 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9198 (t0) REVERT: R 411 GLU cc_start: 0.8068 (pp20) cc_final: 0.7794 (pp20) REVERT: R 452 PHE cc_start: 0.6818 (t80) cc_final: 0.6347 (t80) REVERT: R 453 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7545 (tttp) REVERT: S 36 GLU cc_start: 0.8828 (mp0) cc_final: 0.8607 (mp0) REVERT: S 144 ASN cc_start: 0.8514 (p0) cc_final: 0.8222 (p0) REVERT: S 242 LEU cc_start: 0.9238 (mt) cc_final: 0.8909 (mt) REVERT: S 282 GLU cc_start: 0.7423 (tt0) cc_final: 0.7088 (tt0) REVERT: S 299 MET cc_start: 0.8329 (ttm) cc_final: 0.8079 (ttp) REVERT: T 112 CYS cc_start: 0.7744 (t) cc_final: 0.6898 (t) REVERT: T 117 TYR cc_start: 0.7605 (m-80) cc_final: 0.7398 (m-80) REVERT: T 129 ARG cc_start: 0.7660 (tpp-160) cc_final: 0.7303 (tpt-90) REVERT: T 145 ARG cc_start: 0.8462 (ptp-110) cc_final: 0.7087 (ptp-110) REVERT: T 182 ASN cc_start: 0.8544 (m110) cc_final: 0.7985 (m110) REVERT: T 244 ILE cc_start: 0.8831 (mm) cc_final: 0.8543 (pt) REVERT: T 306 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7932 (tm-30) REVERT: T 453 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7795 (ttmm) REVERT: U 33 ASP cc_start: 0.7793 (t0) cc_final: 0.7193 (t70) REVERT: U 35 SER cc_start: 0.8762 (t) cc_final: 0.8444 (t) REVERT: U 36 GLU cc_start: 0.8748 (mp0) cc_final: 0.7033 (mp0) REVERT: U 219 MET cc_start: 0.8667 (ttm) cc_final: 0.8342 (ttm) REVERT: V 100 ILE cc_start: 0.9040 (mp) cc_final: 0.8747 (mp) REVERT: V 129 ARG cc_start: 0.7567 (tpt-90) cc_final: 0.7339 (tpt-90) REVERT: V 158 ASP cc_start: 0.7468 (t70) cc_final: 0.7075 (t70) REVERT: V 182 ASN cc_start: 0.8632 (m110) cc_final: 0.7495 (m-40) REVERT: V 196 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6669 (mt-10) REVERT: V 202 ASP cc_start: 0.7940 (t70) cc_final: 0.7730 (t0) REVERT: V 242 MET cc_start: 0.8857 (tpt) cc_final: 0.8313 (tpt) REVERT: V 306 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7744 (tm-30) REVERT: V 329 MET cc_start: 0.8656 (mtp) cc_final: 0.8297 (mtt) REVERT: V 448 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7944 (tp30) REVERT: V 452 PHE cc_start: 0.7256 (t80) cc_final: 0.5971 (t80) REVERT: V 453 LYS cc_start: 0.7530 (ttmt) cc_final: 0.6833 (tttp) REVERT: X 254 GLU cc_start: 0.6900 (tt0) cc_final: 0.6690 (tt0) REVERT: X 269 MET cc_start: 0.8123 (ptt) cc_final: 0.7744 (tmm) REVERT: X 282 GLU cc_start: 0.7503 (tt0) cc_final: 0.7166 (tt0) outliers start: 10 outliers final: 0 residues processed: 2024 average time/residue: 0.6217 time to fit residues: 2131.6218 Evaluate side-chains 1673 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1669 time to evaluate : 5.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 265 optimal weight: 0.6980 chunk 710 optimal weight: 0.0970 chunk 155 optimal weight: 0.5980 chunk 463 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 789 optimal weight: 4.9990 chunk 655 optimal weight: 6.9990 chunk 365 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 414 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 113 GLN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 HIS W 214 ASN B 113 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS E 214 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN H 180 GLN ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 279 GLN J 284 HIS K 214 ASN ** L 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 ASN N 113 GLN N 180 GLN ** N 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 HIS ** O 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 279 GLN P 284 HIS Q 214 ASN R 113 GLN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 HIS ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN T 113 GLN T 180 GLN ** T 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 HIS ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 HIS ** X 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 69108 Z= 0.180 Angle : 0.522 10.759 93204 Z= 0.279 Chirality : 0.041 0.136 9840 Planarity : 0.004 0.058 12240 Dihedral : 4.621 21.800 9120 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.11 % Allowed : 1.72 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.22 (0.09), residues: 8280 helix: 0.93 (0.09), residues: 3216 sheet: -1.33 (0.14), residues: 1236 loop : 0.15 (0.10), residues: 3828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 146 HIS 0.004 0.001 HIS S 77 PHE 0.020 0.001 PHE U 133 TYR 0.014 0.001 TYR P 491 ARG 0.006 0.001 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2188 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2180 time to evaluate : 5.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8880 (mp) cc_final: 0.8602 (mp) REVERT: A 112 CYS cc_start: 0.7285 (t) cc_final: 0.7071 (t) REVERT: A 141 GLU cc_start: 0.5915 (pt0) cc_final: 0.5648 (mt-10) REVERT: A 143 MET cc_start: 0.7537 (mmm) cc_final: 0.7274 (mmm) REVERT: A 158 ASP cc_start: 0.7347 (t70) cc_final: 0.7029 (t70) REVERT: A 182 ASN cc_start: 0.8650 (m110) cc_final: 0.7934 (m-40) REVERT: A 411 GLU cc_start: 0.8073 (pp20) cc_final: 0.7702 (pp20) REVERT: A 428 PHE cc_start: 0.8808 (t80) cc_final: 0.8538 (t80) REVERT: A 448 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7891 (tp30) REVERT: A 453 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7549 (tttp) REVERT: A 462 GLN cc_start: 0.7753 (tp40) cc_final: 0.7119 (tt0) REVERT: W 144 ASN cc_start: 0.8438 (p0) cc_final: 0.8154 (p0) REVERT: W 242 LEU cc_start: 0.9237 (mt) cc_final: 0.9012 (mt) REVERT: W 282 GLU cc_start: 0.7263 (tt0) cc_final: 0.7040 (tt0) REVERT: B 112 CYS cc_start: 0.7476 (t) cc_final: 0.7224 (t) REVERT: B 145 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.7343 (ptp-110) REVERT: B 224 VAL cc_start: 0.9315 (p) cc_final: 0.9035 (t) REVERT: B 306 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7830 (tm-30) REVERT: B 453 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7773 (ttmm) REVERT: C 146 TRP cc_start: 0.9206 (p90) cc_final: 0.8966 (p90) REVERT: C 217 TRP cc_start: 0.8584 (p90) cc_final: 0.8221 (p90) REVERT: C 282 GLU cc_start: 0.7160 (tt0) cc_final: 0.6893 (tt0) REVERT: D 100 ILE cc_start: 0.8917 (mp) cc_final: 0.8677 (mp) REVERT: D 182 ASN cc_start: 0.8672 (m110) cc_final: 0.8036 (m-40) REVERT: D 196 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6584 (mt-10) REVERT: D 244 ILE cc_start: 0.8773 (mm) cc_final: 0.8524 (pt) REVERT: D 329 MET cc_start: 0.8646 (mtp) cc_final: 0.8366 (mtt) REVERT: D 453 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6915 (ttmm) REVERT: E 107 GLU cc_start: 0.8237 (tp30) cc_final: 0.7987 (tp30) REVERT: E 146 TRP cc_start: 0.9171 (p90) cc_final: 0.8928 (p90) REVERT: E 217 TRP cc_start: 0.8908 (p90) cc_final: 0.8401 (p90) REVERT: E 282 GLU cc_start: 0.7397 (tt0) cc_final: 0.7113 (tt0) REVERT: F 98 ASN cc_start: 0.8918 (m-40) cc_final: 0.8718 (m-40) REVERT: F 100 ILE cc_start: 0.8910 (mp) cc_final: 0.8639 (mp) REVERT: F 112 CYS cc_start: 0.7316 (t) cc_final: 0.7104 (t) REVERT: F 145 ARG cc_start: 0.8279 (ptp-110) cc_final: 0.6814 (ptp-110) REVERT: F 158 ASP cc_start: 0.7385 (t70) cc_final: 0.7048 (t70) REVERT: F 182 ASN cc_start: 0.8651 (m110) cc_final: 0.7858 (m-40) REVERT: F 448 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7901 (tp30) REVERT: F 453 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7563 (tttp) REVERT: G 144 ASN cc_start: 0.8364 (p0) cc_final: 0.8109 (p0) REVERT: G 242 LEU cc_start: 0.9252 (mt) cc_final: 0.9015 (mt) REVERT: G 282 GLU cc_start: 0.7249 (tt0) cc_final: 0.7022 (tt0) REVERT: H 145 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7363 (ptp-110) REVERT: H 224 VAL cc_start: 0.9302 (p) cc_final: 0.9062 (m) REVERT: H 306 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7774 (tm-30) REVERT: H 453 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7753 (ttmm) REVERT: I 146 TRP cc_start: 0.9228 (p90) cc_final: 0.9011 (p90) REVERT: I 217 TRP cc_start: 0.8605 (p90) cc_final: 0.8246 (p90) REVERT: I 282 GLU cc_start: 0.7201 (tt0) cc_final: 0.6986 (tt0) REVERT: J 100 ILE cc_start: 0.8917 (mp) cc_final: 0.8665 (mp) REVERT: J 129 ARG cc_start: 0.7059 (tpt-90) cc_final: 0.6848 (tpt-90) REVERT: J 182 ASN cc_start: 0.8649 (m110) cc_final: 0.8018 (m-40) REVERT: J 196 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6496 (mt-10) REVERT: J 202 ASP cc_start: 0.7938 (t70) cc_final: 0.7221 (t70) REVERT: J 244 ILE cc_start: 0.8786 (mm) cc_final: 0.8537 (pt) REVERT: J 445 LEU cc_start: 0.8557 (tp) cc_final: 0.8357 (tp) REVERT: J 448 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8047 (tp30) REVERT: J 453 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7269 (tttp) REVERT: K 107 GLU cc_start: 0.8244 (tp30) cc_final: 0.8009 (tp30) REVERT: K 146 TRP cc_start: 0.9174 (p90) cc_final: 0.8929 (p90) REVERT: K 217 TRP cc_start: 0.8906 (p90) cc_final: 0.8406 (p90) REVERT: K 282 GLU cc_start: 0.7379 (tt0) cc_final: 0.7056 (tt0) REVERT: L 98 ASN cc_start: 0.8918 (m-40) cc_final: 0.8710 (m-40) REVERT: L 100 ILE cc_start: 0.8901 (mp) cc_final: 0.8640 (mp) REVERT: L 112 CYS cc_start: 0.7520 (t) cc_final: 0.6494 (t) REVERT: L 113 GLN cc_start: 0.7303 (mm-40) cc_final: 0.7032 (mm110) REVERT: L 117 TYR cc_start: 0.7552 (m-80) cc_final: 0.6941 (m-80) REVERT: L 145 ARG cc_start: 0.8414 (ptp90) cc_final: 0.8130 (ttm110) REVERT: L 158 ASP cc_start: 0.7368 (t70) cc_final: 0.7012 (t70) REVERT: L 182 ASN cc_start: 0.8641 (m110) cc_final: 0.7851 (m-40) REVERT: L 411 GLU cc_start: 0.8096 (pp20) cc_final: 0.7705 (pp20) REVERT: L 426 TYR cc_start: 0.7941 (m-10) cc_final: 0.7553 (m-10) REVERT: L 448 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7896 (tp30) REVERT: L 453 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7597 (tttp) REVERT: M 144 ASN cc_start: 0.8355 (p0) cc_final: 0.8097 (p0) REVERT: M 242 LEU cc_start: 0.9251 (mt) cc_final: 0.9021 (mt) REVERT: M 282 GLU cc_start: 0.7287 (tt0) cc_final: 0.7027 (tt0) REVERT: N 112 CYS cc_start: 0.7490 (t) cc_final: 0.7219 (t) REVERT: N 145 ARG cc_start: 0.8447 (ptp-110) cc_final: 0.7330 (ptp-110) REVERT: N 224 VAL cc_start: 0.9313 (p) cc_final: 0.9055 (m) REVERT: N 306 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7774 (tm-30) REVERT: N 453 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7764 (ttmm) REVERT: O 146 TRP cc_start: 0.9231 (p90) cc_final: 0.9002 (p90) REVERT: O 217 TRP cc_start: 0.8582 (p90) cc_final: 0.8214 (p90) REVERT: P 100 ILE cc_start: 0.8922 (mp) cc_final: 0.8662 (mp) REVERT: P 125 GLU cc_start: 0.8611 (tt0) cc_final: 0.8258 (pt0) REVERT: P 182 ASN cc_start: 0.8659 (m110) cc_final: 0.8025 (m-40) REVERT: P 196 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6496 (mt-10) REVERT: P 202 ASP cc_start: 0.7931 (t70) cc_final: 0.7201 (t70) REVERT: P 244 ILE cc_start: 0.8795 (mm) cc_final: 0.8535 (pt) REVERT: P 329 MET cc_start: 0.8535 (mtp) cc_final: 0.8325 (mtm) REVERT: P 448 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8048 (tp30) REVERT: P 453 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7276 (tttp) REVERT: Q 36 GLU cc_start: 0.8735 (mp0) cc_final: 0.8324 (mp0) REVERT: Q 107 GLU cc_start: 0.8259 (tp30) cc_final: 0.8020 (tp30) REVERT: Q 146 TRP cc_start: 0.9177 (p90) cc_final: 0.8928 (p90) REVERT: Q 217 TRP cc_start: 0.8902 (p90) cc_final: 0.8417 (p90) REVERT: Q 282 GLU cc_start: 0.7404 (tt0) cc_final: 0.7082 (tt0) REVERT: R 100 ILE cc_start: 0.8909 (mp) cc_final: 0.8637 (mp) REVERT: R 112 CYS cc_start: 0.7517 (t) cc_final: 0.6455 (t) REVERT: R 113 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7006 (mm110) REVERT: R 158 ASP cc_start: 0.7403 (t70) cc_final: 0.7047 (t70) REVERT: R 182 ASN cc_start: 0.8626 (m110) cc_final: 0.7237 (m-40) REVERT: R 242 MET cc_start: 0.9022 (tpt) cc_final: 0.8742 (tpt) REVERT: R 411 GLU cc_start: 0.8082 (pp20) cc_final: 0.7680 (pp20) REVERT: R 426 TYR cc_start: 0.7798 (m-10) cc_final: 0.7320 (m-10) REVERT: R 448 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8184 (tp30) REVERT: R 452 PHE cc_start: 0.6746 (t80) cc_final: 0.6268 (t80) REVERT: R 453 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7561 (tttp) REVERT: S 144 ASN cc_start: 0.8373 (p0) cc_final: 0.8150 (p0) REVERT: S 242 LEU cc_start: 0.9239 (mt) cc_final: 0.9020 (mt) REVERT: S 282 GLU cc_start: 0.7301 (tt0) cc_final: 0.7037 (tt0) REVERT: T 112 CYS cc_start: 0.7470 (t) cc_final: 0.7217 (t) REVERT: T 145 ARG cc_start: 0.8454 (ptp-110) cc_final: 0.7341 (ptp-110) REVERT: T 224 VAL cc_start: 0.9317 (p) cc_final: 0.9067 (m) REVERT: T 306 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7775 (tm-30) REVERT: T 453 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7782 (ttmm) REVERT: U 146 TRP cc_start: 0.9234 (p90) cc_final: 0.9001 (p90) REVERT: U 217 TRP cc_start: 0.8576 (p90) cc_final: 0.8212 (p90) REVERT: U 282 GLU cc_start: 0.7120 (tt0) cc_final: 0.6874 (tt0) REVERT: V 100 ILE cc_start: 0.8922 (mp) cc_final: 0.8659 (mp) REVERT: V 129 ARG cc_start: 0.7506 (tpt-90) cc_final: 0.7241 (tpt-90) REVERT: V 182 ASN cc_start: 0.8670 (m110) cc_final: 0.8032 (m-40) REVERT: V 196 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6505 (mt-10) REVERT: V 202 ASP cc_start: 0.7945 (t70) cc_final: 0.7200 (t70) REVERT: V 244 ILE cc_start: 0.8786 (mm) cc_final: 0.8533 (pt) REVERT: V 329 MET cc_start: 0.8513 (mtp) cc_final: 0.8278 (mtm) REVERT: V 446 LYS cc_start: 0.7927 (tttt) cc_final: 0.7675 (pttp) REVERT: V 448 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7760 (tp30) REVERT: V 453 LYS cc_start: 0.7476 (ttmt) cc_final: 0.6740 (tttp) REVERT: X 36 GLU cc_start: 0.8740 (mp0) cc_final: 0.8330 (mp0) REVERT: X 146 TRP cc_start: 0.9174 (p90) cc_final: 0.8910 (p90) REVERT: X 217 TRP cc_start: 0.8894 (p90) cc_final: 0.8399 (p90) REVERT: X 282 GLU cc_start: 0.7358 (tt0) cc_final: 0.7076 (tt0) outliers start: 8 outliers final: 0 residues processed: 2188 average time/residue: 0.6350 time to fit residues: 2340.2629 Evaluate side-chains 1776 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1776 time to evaluate : 5.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 761 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 449 optimal weight: 1.9990 chunk 576 optimal weight: 0.0970 chunk 446 optimal weight: 3.9990 chunk 664 optimal weight: 6.9990 chunk 440 optimal weight: 0.1980 chunk 786 optimal weight: 0.6980 chunk 492 optimal weight: 0.9980 chunk 479 optimal weight: 8.9990 chunk 363 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 ASN W 279 GLN B 284 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN F 284 HIS ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 ASN H 284 HIS ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN L 284 HIS ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 ASN N 284 HIS ** N 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN Q 214 ASN R 284 HIS ** R 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 214 ASN S 279 GLN T 284 HIS ** T 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 279 GLN ** V 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 69108 Z= 0.153 Angle : 0.505 10.147 93204 Z= 0.269 Chirality : 0.041 0.132 9840 Planarity : 0.004 0.037 12240 Dihedral : 4.331 22.649 9120 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.23 % Allowed : 1.49 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.46 (0.09), residues: 8280 helix: 1.13 (0.09), residues: 3228 sheet: -1.22 (0.14), residues: 1248 loop : 0.30 (0.10), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 145 HIS 0.006 0.001 HIS S 77 PHE 0.024 0.001 PHE K 133 TYR 0.024 0.001 TYR B 117 ARG 0.009 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2213 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 2196 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.5462 (ptm) cc_final: 0.4153 (ptm) REVERT: A 100 ILE cc_start: 0.8841 (mp) cc_final: 0.8596 (mp) REVERT: A 112 CYS cc_start: 0.7458 (t) cc_final: 0.6596 (t) REVERT: A 113 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7185 (mm110) REVERT: A 143 MET cc_start: 0.7447 (mtt) cc_final: 0.7174 (mmm) REVERT: A 158 ASP cc_start: 0.7279 (t70) cc_final: 0.7009 (t70) REVERT: A 182 ASN cc_start: 0.8658 (m110) cc_final: 0.7918 (m-40) REVERT: A 329 MET cc_start: 0.8556 (mtm) cc_final: 0.8330 (mtt) REVERT: A 411 GLU cc_start: 0.8054 (pp20) cc_final: 0.7634 (pp20) REVERT: A 428 PHE cc_start: 0.8765 (t80) cc_final: 0.8442 (t80) REVERT: A 448 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7795 (tp30) REVERT: A 453 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7498 (ttmm) REVERT: A 462 GLN cc_start: 0.7624 (tp40) cc_final: 0.7054 (tt0) REVERT: W 36 GLU cc_start: 0.8692 (mp0) cc_final: 0.8261 (mp0) REVERT: W 144 ASN cc_start: 0.8361 (p0) cc_final: 0.8096 (p0) REVERT: W 217 TRP cc_start: 0.8790 (p90) cc_final: 0.8170 (p90) REVERT: W 270 TYR cc_start: 0.7029 (m-10) cc_final: 0.5956 (m-10) REVERT: W 282 GLU cc_start: 0.7234 (tt0) cc_final: 0.6953 (tt0) REVERT: B 78 MET cc_start: 0.6666 (mmm) cc_final: 0.6159 (ptm) REVERT: B 100 ILE cc_start: 0.8871 (mp) cc_final: 0.8660 (mp) REVERT: B 112 CYS cc_start: 0.7676 (t) cc_final: 0.7330 (t) REVERT: B 145 ARG cc_start: 0.8517 (ptp-110) cc_final: 0.7495 (ptp-110) REVERT: B 161 ARG cc_start: 0.6661 (ttp-170) cc_final: 0.6146 (ttp-170) REVERT: B 202 ASP cc_start: 0.8057 (t70) cc_final: 0.7480 (t0) REVERT: B 224 VAL cc_start: 0.9301 (p) cc_final: 0.9036 (t) REVERT: B 306 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7715 (tm-30) REVERT: B 453 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7676 (ttmm) REVERT: B 487 GLN cc_start: 0.6614 (tp40) cc_final: 0.6390 (tm-30) REVERT: C 56 MET cc_start: 0.8500 (mtm) cc_final: 0.8191 (mtm) REVERT: C 217 TRP cc_start: 0.8604 (p90) cc_final: 0.8210 (p90) REVERT: C 282 GLU cc_start: 0.7071 (tt0) cc_final: 0.6827 (tt0) REVERT: D 100 ILE cc_start: 0.8847 (mp) cc_final: 0.8614 (mp) REVERT: D 158 ASP cc_start: 0.7525 (t0) cc_final: 0.7171 (t70) REVERT: D 182 ASN cc_start: 0.8503 (m110) cc_final: 0.7966 (m-40) REVERT: D 196 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6628 (mt-10) REVERT: D 244 ILE cc_start: 0.8734 (mm) cc_final: 0.8513 (pt) REVERT: D 329 MET cc_start: 0.8714 (mtp) cc_final: 0.8399 (mtt) REVERT: D 359 SER cc_start: 0.9097 (m) cc_final: 0.8895 (m) REVERT: D 453 LYS cc_start: 0.7426 (ttmt) cc_final: 0.6840 (ttmm) REVERT: E 36 GLU cc_start: 0.8721 (mp0) cc_final: 0.8440 (mp0) REVERT: E 146 TRP cc_start: 0.9054 (p90) cc_final: 0.8789 (p90) REVERT: E 217 TRP cc_start: 0.8920 (p90) cc_final: 0.8426 (p90) REVERT: E 282 GLU cc_start: 0.7357 (tt0) cc_final: 0.6968 (tt0) REVERT: F 78 MET cc_start: 0.5478 (ptm) cc_final: 0.4137 (ptm) REVERT: F 100 ILE cc_start: 0.8835 (mp) cc_final: 0.8573 (mp) REVERT: F 112 CYS cc_start: 0.7352 (t) cc_final: 0.7144 (t) REVERT: F 145 ARG cc_start: 0.8153 (ptp-110) cc_final: 0.6853 (ptp-110) REVERT: F 158 ASP cc_start: 0.7281 (t70) cc_final: 0.7035 (t70) REVERT: F 182 ASN cc_start: 0.8802 (m110) cc_final: 0.8076 (m-40) REVERT: F 448 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7833 (tp30) REVERT: F 453 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7509 (ttmm) REVERT: G 36 GLU cc_start: 0.8722 (mp0) cc_final: 0.8308 (mp0) REVERT: G 144 ASN cc_start: 0.8315 (p0) cc_final: 0.8009 (p0) REVERT: G 217 TRP cc_start: 0.8774 (p90) cc_final: 0.8180 (p90) REVERT: G 270 TYR cc_start: 0.7014 (m-10) cc_final: 0.5937 (m-10) REVERT: G 282 GLU cc_start: 0.7199 (tt0) cc_final: 0.6923 (tt0) REVERT: H 100 ILE cc_start: 0.8844 (mp) cc_final: 0.8641 (mp) REVERT: H 145 ARG cc_start: 0.8537 (ptp-110) cc_final: 0.7495 (ptp-110) REVERT: H 197 LYS cc_start: 0.6545 (mtmt) cc_final: 0.6241 (ptmt) REVERT: H 202 ASP cc_start: 0.8040 (t70) cc_final: 0.7462 (t0) REVERT: H 226 VAL cc_start: 0.9333 (t) cc_final: 0.9123 (t) REVERT: H 305 LEU cc_start: 0.9078 (mt) cc_final: 0.8525 (mt) REVERT: H 453 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7664 (ttmm) REVERT: H 487 GLN cc_start: 0.6609 (tp40) cc_final: 0.6392 (tm-30) REVERT: I 56 MET cc_start: 0.8515 (mtm) cc_final: 0.8205 (mtm) REVERT: I 217 TRP cc_start: 0.8601 (p90) cc_final: 0.8192 (p90) REVERT: I 222 GLU cc_start: 0.8347 (mp0) cc_final: 0.7933 (mp0) REVERT: J 100 ILE cc_start: 0.8847 (mp) cc_final: 0.8641 (mp) REVERT: J 158 ASP cc_start: 0.7584 (t0) cc_final: 0.7176 (t70) REVERT: J 182 ASN cc_start: 0.8651 (m110) cc_final: 0.7743 (m-40) REVERT: J 196 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6536 (mt-10) REVERT: J 202 ASP cc_start: 0.7852 (t70) cc_final: 0.7097 (t70) REVERT: J 242 MET cc_start: 0.8716 (tpt) cc_final: 0.8194 (tpt) REVERT: J 359 SER cc_start: 0.9107 (m) cc_final: 0.8899 (m) REVERT: J 448 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7806 (tm-30) REVERT: J 453 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7249 (ttmm) REVERT: J 462 GLN cc_start: 0.7598 (tp40) cc_final: 0.7353 (tp40) REVERT: K 36 GLU cc_start: 0.8736 (mp0) cc_final: 0.8459 (mp0) REVERT: K 146 TRP cc_start: 0.9063 (p90) cc_final: 0.8798 (p90) REVERT: K 217 TRP cc_start: 0.8911 (p90) cc_final: 0.8379 (p90) REVERT: K 282 GLU cc_start: 0.7401 (tt0) cc_final: 0.7009 (tt0) REVERT: L 100 ILE cc_start: 0.8856 (mp) cc_final: 0.8634 (mp) REVERT: L 112 CYS cc_start: 0.7599 (t) cc_final: 0.7208 (t) REVERT: L 138 LYS cc_start: 0.6743 (mttp) cc_final: 0.6385 (mttm) REVERT: L 158 ASP cc_start: 0.7273 (t70) cc_final: 0.7043 (t70) REVERT: L 182 ASN cc_start: 0.8813 (m110) cc_final: 0.8069 (m-40) REVERT: L 411 GLU cc_start: 0.8075 (pp20) cc_final: 0.7643 (pp20) REVERT: L 428 PHE cc_start: 0.8792 (t80) cc_final: 0.8581 (t80) REVERT: L 448 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7813 (tp30) REVERT: L 453 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7322 (ttmm) REVERT: M 36 GLU cc_start: 0.8716 (mp0) cc_final: 0.8300 (mp0) REVERT: M 144 ASN cc_start: 0.8305 (p0) cc_final: 0.7984 (p0) REVERT: M 217 TRP cc_start: 0.8776 (p90) cc_final: 0.8222 (p90) REVERT: M 270 TYR cc_start: 0.7019 (m-10) cc_final: 0.5941 (m-10) REVERT: M 282 GLU cc_start: 0.7239 (tt0) cc_final: 0.6930 (tt0) REVERT: N 100 ILE cc_start: 0.8875 (mp) cc_final: 0.8674 (mp) REVERT: N 145 ARG cc_start: 0.8493 (ptp-110) cc_final: 0.7477 (ptp-110) REVERT: N 161 ARG cc_start: 0.6701 (ttp-170) cc_final: 0.6168 (ttp-170) REVERT: N 202 ASP cc_start: 0.8059 (t70) cc_final: 0.7581 (t0) REVERT: N 224 VAL cc_start: 0.9292 (p) cc_final: 0.9082 (t) REVERT: N 226 VAL cc_start: 0.9313 (t) cc_final: 0.9100 (t) REVERT: N 306 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7763 (tm-30) REVERT: N 453 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7675 (ttmm) REVERT: N 487 GLN cc_start: 0.6611 (tp40) cc_final: 0.6399 (tm-30) REVERT: O 56 MET cc_start: 0.8509 (mtm) cc_final: 0.8205 (mtm) REVERT: O 217 TRP cc_start: 0.8599 (p90) cc_final: 0.8164 (p90) REVERT: P 100 ILE cc_start: 0.8843 (mp) cc_final: 0.8635 (mp) REVERT: P 125 GLU cc_start: 0.8485 (tt0) cc_final: 0.8276 (pt0) REVERT: P 158 ASP cc_start: 0.7540 (t0) cc_final: 0.7182 (t70) REVERT: P 182 ASN cc_start: 0.8632 (m110) cc_final: 0.7737 (m-40) REVERT: P 196 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6545 (mt-10) REVERT: P 202 ASP cc_start: 0.7830 (t70) cc_final: 0.7065 (t70) REVERT: P 242 MET cc_start: 0.8722 (tpt) cc_final: 0.8197 (tpt) REVERT: P 329 MET cc_start: 0.8674 (mtp) cc_final: 0.8352 (mtt) REVERT: P 359 SER cc_start: 0.9096 (m) cc_final: 0.8895 (m) REVERT: P 448 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7798 (tm-30) REVERT: P 453 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7242 (ttmm) REVERT: P 462 GLN cc_start: 0.7596 (tp40) cc_final: 0.7366 (tp40) REVERT: Q 146 TRP cc_start: 0.9057 (p90) cc_final: 0.8791 (p90) REVERT: Q 217 TRP cc_start: 0.8946 (p90) cc_final: 0.8383 (p90) REVERT: Q 282 GLU cc_start: 0.7406 (tt0) cc_final: 0.7063 (tt0) REVERT: R 78 MET cc_start: 0.5529 (ptm) cc_final: 0.4309 (ptm) REVERT: R 100 ILE cc_start: 0.8842 (mp) cc_final: 0.8602 (mp) REVERT: R 112 CYS cc_start: 0.7588 (t) cc_final: 0.7214 (t) REVERT: R 138 LYS cc_start: 0.6697 (mttp) cc_final: 0.6347 (mttm) REVERT: R 158 ASP cc_start: 0.7303 (t70) cc_final: 0.7061 (t70) REVERT: R 182 ASN cc_start: 0.8653 (m110) cc_final: 0.7394 (m-40) REVERT: R 249 THR cc_start: 0.8752 (p) cc_final: 0.8544 (p) REVERT: R 411 GLU cc_start: 0.8062 (pp20) cc_final: 0.7595 (pp20) REVERT: R 428 PHE cc_start: 0.8784 (t80) cc_final: 0.8533 (t80) REVERT: R 448 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8032 (tp30) REVERT: R 452 PHE cc_start: 0.6691 (t80) cc_final: 0.6205 (t80) REVERT: R 453 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7392 (tttp) REVERT: S 36 GLU cc_start: 0.8706 (mp0) cc_final: 0.8298 (mp0) REVERT: S 144 ASN cc_start: 0.8367 (p0) cc_final: 0.8103 (p0) REVERT: S 217 TRP cc_start: 0.8779 (p90) cc_final: 0.8181 (p90) REVERT: S 270 TYR cc_start: 0.7032 (m-10) cc_final: 0.5947 (m-10) REVERT: S 282 GLU cc_start: 0.7236 (tt0) cc_final: 0.6899 (tt0) REVERT: T 112 CYS cc_start: 0.7561 (t) cc_final: 0.7300 (t) REVERT: T 145 ARG cc_start: 0.8488 (ptp-110) cc_final: 0.7478 (ptp-110) REVERT: T 161 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.6166 (ttp-170) REVERT: T 202 ASP cc_start: 0.8046 (t70) cc_final: 0.7524 (t0) REVERT: T 224 VAL cc_start: 0.9288 (p) cc_final: 0.9073 (t) REVERT: T 226 VAL cc_start: 0.9328 (t) cc_final: 0.9117 (t) REVERT: T 306 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7770 (tm-30) REVERT: T 453 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7594 (tttp) REVERT: T 487 GLN cc_start: 0.6613 (tp40) cc_final: 0.6395 (tm-30) REVERT: U 56 MET cc_start: 0.8511 (mtm) cc_final: 0.8201 (mtm) REVERT: U 217 TRP cc_start: 0.8594 (p90) cc_final: 0.8167 (p90) REVERT: U 282 GLU cc_start: 0.7042 (tt0) cc_final: 0.6811 (tt0) REVERT: V 100 ILE cc_start: 0.8838 (mp) cc_final: 0.8633 (mp) REVERT: V 125 GLU cc_start: 0.9024 (pt0) cc_final: 0.8823 (pt0) REVERT: V 158 ASP cc_start: 0.7493 (t0) cc_final: 0.7101 (t70) REVERT: V 182 ASN cc_start: 0.8656 (m110) cc_final: 0.7732 (m-40) REVERT: V 196 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6560 (mt-10) REVERT: V 202 ASP cc_start: 0.7846 (t70) cc_final: 0.7064 (t70) REVERT: V 242 MET cc_start: 0.8699 (tpt) cc_final: 0.8094 (tpt) REVERT: V 329 MET cc_start: 0.8659 (mtp) cc_final: 0.8344 (mtt) REVERT: V 359 SER cc_start: 0.9085 (m) cc_final: 0.8866 (m) REVERT: V 453 LYS cc_start: 0.7387 (ttmt) cc_final: 0.6301 (ttmm) REVERT: X 146 TRP cc_start: 0.9044 (p90) cc_final: 0.8787 (p90) REVERT: X 217 TRP cc_start: 0.8911 (p90) cc_final: 0.8411 (p90) REVERT: X 282 GLU cc_start: 0.7389 (tt0) cc_final: 0.7075 (tt0) outliers start: 17 outliers final: 8 residues processed: 2205 average time/residue: 0.6285 time to fit residues: 2351.2488 Evaluate side-chains 1824 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1816 time to evaluate : 5.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 486 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 469 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 500 optimal weight: 5.9990 chunk 535 optimal weight: 0.7980 chunk 388 optimal weight: 0.0050 chunk 73 optimal weight: 0.5980 chunk 618 optimal weight: 4.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 279 GLN B 107 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** H 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 GLN ** N 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN P 284 HIS ** P 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 ASN ** R 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 279 GLN T 107 GLN ** T 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 279 GLN V 284 HIS ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 69108 Z= 0.203 Angle : 0.540 10.273 93204 Z= 0.287 Chirality : 0.041 0.133 9840 Planarity : 0.004 0.035 12240 Dihedral : 4.382 21.269 9120 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.12 % Allowed : 0.78 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.41 (0.09), residues: 8280 helix: 1.13 (0.09), residues: 3216 sheet: -1.23 (0.14), residues: 1248 loop : 0.23 (0.10), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 312 HIS 0.004 0.001 HIS W 77 PHE 0.024 0.001 PHE O 133 TYR 0.016 0.001 TYR B 422 ARG 0.010 0.001 ARG R 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2172 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2163 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8917 (mp) cc_final: 0.8668 (mp) REVERT: A 112 CYS cc_start: 0.7485 (t) cc_final: 0.6532 (t) REVERT: A 113 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7158 (mm110) REVERT: A 158 ASP cc_start: 0.7405 (t70) cc_final: 0.7039 (t70) REVERT: A 182 ASN cc_start: 0.8714 (m110) cc_final: 0.7964 (m-40) REVERT: A 249 THR cc_start: 0.8830 (p) cc_final: 0.8605 (p) REVERT: A 411 GLU cc_start: 0.8107 (pp20) cc_final: 0.7661 (pp20) REVERT: A 428 PHE cc_start: 0.8788 (t80) cc_final: 0.8501 (t80) REVERT: A 452 PHE cc_start: 0.6672 (t80) cc_final: 0.6332 (t80) REVERT: A 453 LYS cc_start: 0.7990 (ttmm) cc_final: 0.6601 (ttmm) REVERT: A 462 GLN cc_start: 0.7651 (tp40) cc_final: 0.7012 (tt0) REVERT: W 33 ASP cc_start: 0.7640 (t0) cc_final: 0.7235 (t70) REVERT: W 36 GLU cc_start: 0.8746 (mp0) cc_final: 0.7856 (mp0) REVERT: W 144 ASN cc_start: 0.8366 (p0) cc_final: 0.8129 (p0) REVERT: W 217 TRP cc_start: 0.8784 (p90) cc_final: 0.8299 (p90) REVERT: W 270 TYR cc_start: 0.7243 (m-10) cc_final: 0.6332 (m-10) REVERT: B 78 MET cc_start: 0.6701 (mmm) cc_final: 0.6208 (ptm) REVERT: B 145 ARG cc_start: 0.8579 (ptp-110) cc_final: 0.7481 (ptp-110) REVERT: B 182 ASN cc_start: 0.8634 (m110) cc_final: 0.7882 (m-40) REVERT: B 197 LYS cc_start: 0.6528 (mtmt) cc_final: 0.6269 (mtmt) REVERT: B 202 ASP cc_start: 0.8037 (t70) cc_final: 0.7511 (t0) REVERT: B 224 VAL cc_start: 0.9265 (p) cc_final: 0.9039 (t) REVERT: B 306 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7697 (tm-30) REVERT: B 453 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7577 (tttp) REVERT: C 33 ASP cc_start: 0.7753 (t0) cc_final: 0.7546 (t0) REVERT: C 36 GLU cc_start: 0.8763 (mp0) cc_final: 0.7789 (mp0) REVERT: C 56 MET cc_start: 0.8532 (mtm) cc_final: 0.8285 (mtm) REVERT: C 149 GLU cc_start: 0.7937 (mp0) cc_final: 0.6626 (mp0) REVERT: C 217 TRP cc_start: 0.8671 (p90) cc_final: 0.8239 (p90) REVERT: C 282 GLU cc_start: 0.7152 (tt0) cc_final: 0.6916 (tt0) REVERT: D 100 ILE cc_start: 0.8878 (mp) cc_final: 0.8631 (mp) REVERT: D 158 ASP cc_start: 0.7598 (t0) cc_final: 0.7053 (t70) REVERT: D 182 ASN cc_start: 0.8466 (m110) cc_final: 0.7911 (m-40) REVERT: D 196 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6476 (mt-10) REVERT: D 244 ILE cc_start: 0.8728 (mm) cc_final: 0.8492 (pt) REVERT: D 284 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7624 (m90) REVERT: D 310 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7096 (ttm170) REVERT: D 329 MET cc_start: 0.8710 (mtp) cc_final: 0.8356 (mtm) REVERT: D 442 LEU cc_start: 0.8278 (mt) cc_final: 0.8054 (mt) REVERT: D 453 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6841 (ttmm) REVERT: E 36 GLU cc_start: 0.8726 (mp0) cc_final: 0.8406 (mp0) REVERT: E 146 TRP cc_start: 0.9136 (p90) cc_final: 0.8864 (p90) REVERT: E 217 TRP cc_start: 0.8916 (p90) cc_final: 0.8443 (p90) REVERT: E 282 GLU cc_start: 0.7334 (tt0) cc_final: 0.6936 (tt0) REVERT: F 100 ILE cc_start: 0.8910 (mp) cc_final: 0.8670 (mp) REVERT: F 112 CYS cc_start: 0.7254 (t) cc_final: 0.7030 (t) REVERT: F 145 ARG cc_start: 0.8198 (ptp-110) cc_final: 0.6926 (ptp-110) REVERT: F 158 ASP cc_start: 0.7455 (t70) cc_final: 0.7110 (t70) REVERT: F 182 ASN cc_start: 0.8647 (m110) cc_final: 0.7585 (m-40) REVERT: F 249 THR cc_start: 0.8831 (p) cc_final: 0.8577 (p) REVERT: F 305 LEU cc_start: 0.9143 (mt) cc_final: 0.8622 (mt) REVERT: F 452 PHE cc_start: 0.6679 (t80) cc_final: 0.6457 (t80) REVERT: F 453 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7536 (ttmm) REVERT: G 36 GLU cc_start: 0.8763 (mp0) cc_final: 0.8381 (mp0) REVERT: G 144 ASN cc_start: 0.8360 (p0) cc_final: 0.8082 (p0) REVERT: G 217 TRP cc_start: 0.8771 (p90) cc_final: 0.8288 (p90) REVERT: G 270 TYR cc_start: 0.7252 (m-10) cc_final: 0.6319 (m-10) REVERT: G 282 GLU cc_start: 0.7234 (tt0) cc_final: 0.7027 (tt0) REVERT: H 78 MET cc_start: 0.6715 (mmm) cc_final: 0.6219 (ptm) REVERT: H 145 ARG cc_start: 0.8599 (ptp-110) cc_final: 0.7555 (ptp-110) REVERT: H 182 ASN cc_start: 0.8651 (m110) cc_final: 0.7450 (m-40) REVERT: H 202 ASP cc_start: 0.8007 (t70) cc_final: 0.7487 (t0) REVERT: H 453 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7600 (tttp) REVERT: I 56 MET cc_start: 0.8545 (mtm) cc_final: 0.8298 (mtm) REVERT: I 149 GLU cc_start: 0.7936 (mp0) cc_final: 0.7682 (mt-10) REVERT: I 217 TRP cc_start: 0.8669 (p90) cc_final: 0.8242 (p90) REVERT: J 100 ILE cc_start: 0.8869 (mp) cc_final: 0.8639 (mp) REVERT: J 158 ASP cc_start: 0.7649 (t0) cc_final: 0.7052 (t70) REVERT: J 182 ASN cc_start: 0.8646 (m110) cc_final: 0.7643 (m-40) REVERT: J 196 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6479 (mt-10) REVERT: J 202 ASP cc_start: 0.7862 (t70) cc_final: 0.7652 (t70) REVERT: J 242 MET cc_start: 0.8747 (tpt) cc_final: 0.8024 (tpt) REVERT: J 284 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7632 (m90) REVERT: J 359 SER cc_start: 0.9143 (m) cc_final: 0.8936 (m) REVERT: J 448 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7781 (tm-30) REVERT: J 453 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7099 (tttp) REVERT: J 462 GLN cc_start: 0.7559 (tp40) cc_final: 0.7346 (tp40) REVERT: K 36 GLU cc_start: 0.8728 (mp0) cc_final: 0.8423 (mp0) REVERT: K 146 TRP cc_start: 0.9145 (p90) cc_final: 0.8874 (p90) REVERT: K 217 TRP cc_start: 0.8900 (p90) cc_final: 0.8386 (p90) REVERT: K 282 GLU cc_start: 0.7297 (tt0) cc_final: 0.6909 (tt0) REVERT: L 100 ILE cc_start: 0.8918 (mp) cc_final: 0.8681 (mp) REVERT: L 112 CYS cc_start: 0.7575 (t) cc_final: 0.7228 (t) REVERT: L 117 TYR cc_start: 0.7511 (m-80) cc_final: 0.7234 (m-10) REVERT: L 158 ASP cc_start: 0.7453 (t70) cc_final: 0.7122 (t70) REVERT: L 182 ASN cc_start: 0.8642 (m110) cc_final: 0.7589 (m-40) REVERT: L 300 GLN cc_start: 0.7674 (mp10) cc_final: 0.7439 (mp10) REVERT: L 305 LEU cc_start: 0.9150 (mt) cc_final: 0.8657 (mt) REVERT: L 452 PHE cc_start: 0.6689 (t80) cc_final: 0.6438 (t80) REVERT: L 453 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7250 (ttmm) REVERT: M 36 GLU cc_start: 0.8766 (mp0) cc_final: 0.8376 (mp0) REVERT: M 144 ASN cc_start: 0.8355 (p0) cc_final: 0.8069 (p0) REVERT: M 217 TRP cc_start: 0.8793 (p90) cc_final: 0.8296 (p90) REVERT: M 270 TYR cc_start: 0.7253 (m-10) cc_final: 0.6324 (m-10) REVERT: M 282 GLU cc_start: 0.7263 (tt0) cc_final: 0.7046 (tt0) REVERT: N 78 MET cc_start: 0.6696 (mmm) cc_final: 0.6211 (ptm) REVERT: N 100 ILE cc_start: 0.8873 (mp) cc_final: 0.8670 (mp) REVERT: N 145 ARG cc_start: 0.8566 (ptp-110) cc_final: 0.7532 (ptp-110) REVERT: N 182 ASN cc_start: 0.8591 (m110) cc_final: 0.7845 (m-40) REVERT: N 197 LYS cc_start: 0.6482 (ptmt) cc_final: 0.6137 (pttt) REVERT: N 224 VAL cc_start: 0.9261 (p) cc_final: 0.9018 (t) REVERT: N 306 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7694 (tm-30) REVERT: N 453 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7587 (tttp) REVERT: O 33 ASP cc_start: 0.7740 (t0) cc_final: 0.7537 (t0) REVERT: O 36 GLU cc_start: 0.8775 (mp0) cc_final: 0.7786 (mp0) REVERT: O 56 MET cc_start: 0.8536 (mtm) cc_final: 0.8301 (mtm) REVERT: O 217 TRP cc_start: 0.8648 (p90) cc_final: 0.8201 (p90) REVERT: P 100 ILE cc_start: 0.8865 (mp) cc_final: 0.8631 (mp) REVERT: P 125 GLU cc_start: 0.8609 (tt0) cc_final: 0.8294 (pt0) REVERT: P 158 ASP cc_start: 0.7620 (t0) cc_final: 0.7070 (t70) REVERT: P 182 ASN cc_start: 0.8641 (m110) cc_final: 0.8069 (m-40) REVERT: P 196 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6488 (mt-10) REVERT: P 202 ASP cc_start: 0.7856 (t70) cc_final: 0.7647 (t70) REVERT: P 284 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7631 (m90) REVERT: P 310 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7494 (ttm170) REVERT: P 359 SER cc_start: 0.9138 (m) cc_final: 0.8937 (m) REVERT: P 448 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7772 (tm-30) REVERT: P 453 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7098 (tttp) REVERT: P 462 GLN cc_start: 0.7581 (tp40) cc_final: 0.7373 (tp40) REVERT: Q 36 GLU cc_start: 0.8695 (mp0) cc_final: 0.8340 (mp0) REVERT: Q 146 TRP cc_start: 0.9142 (p90) cc_final: 0.8871 (p90) REVERT: Q 217 TRP cc_start: 0.8913 (p90) cc_final: 0.8395 (p90) REVERT: Q 282 GLU cc_start: 0.7294 (tt0) cc_final: 0.6961 (tt0) REVERT: R 100 ILE cc_start: 0.8915 (mp) cc_final: 0.8673 (mp) REVERT: R 112 CYS cc_start: 0.7577 (t) cc_final: 0.7224 (t) REVERT: R 142 GLU cc_start: 0.7558 (tt0) cc_final: 0.7063 (tt0) REVERT: R 161 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7056 (ttp80) REVERT: R 182 ASN cc_start: 0.8609 (m110) cc_final: 0.7820 (m-40) REVERT: R 249 THR cc_start: 0.8847 (p) cc_final: 0.8606 (p) REVERT: R 300 GLN cc_start: 0.7695 (mp10) cc_final: 0.7438 (mp10) REVERT: R 305 LEU cc_start: 0.9132 (mt) cc_final: 0.8641 (mt) REVERT: R 411 GLU cc_start: 0.8131 (pp20) cc_final: 0.7635 (pp20) REVERT: R 428 PHE cc_start: 0.8785 (t80) cc_final: 0.8458 (t80) REVERT: R 452 PHE cc_start: 0.6725 (t80) cc_final: 0.6281 (t80) REVERT: R 453 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7260 (tttp) REVERT: S 36 GLU cc_start: 0.8752 (mp0) cc_final: 0.8378 (mp0) REVERT: S 144 ASN cc_start: 0.8354 (p0) cc_final: 0.8090 (p0) REVERT: S 217 TRP cc_start: 0.8790 (p90) cc_final: 0.8311 (p90) REVERT: S 270 TYR cc_start: 0.7232 (m-10) cc_final: 0.6309 (m-10) REVERT: T 145 ARG cc_start: 0.8563 (ptp-110) cc_final: 0.7538 (ptp-110) REVERT: T 182 ASN cc_start: 0.8602 (m110) cc_final: 0.7895 (m-40) REVERT: T 197 LYS cc_start: 0.6502 (ptmt) cc_final: 0.6106 (pttt) REVERT: T 202 ASP cc_start: 0.8038 (t70) cc_final: 0.7599 (t0) REVERT: T 224 VAL cc_start: 0.9281 (p) cc_final: 0.9044 (m) REVERT: T 306 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7668 (tm-30) REVERT: T 445 LEU cc_start: 0.8545 (tp) cc_final: 0.8288 (tp) REVERT: T 453 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7597 (tttp) REVERT: U 33 ASP cc_start: 0.7757 (t0) cc_final: 0.7537 (t0) REVERT: U 36 GLU cc_start: 0.8693 (mp0) cc_final: 0.7778 (mp0) REVERT: U 56 MET cc_start: 0.8528 (mtm) cc_final: 0.8290 (mtm) REVERT: U 149 GLU cc_start: 0.8003 (mp0) cc_final: 0.7616 (mt-10) REVERT: U 217 TRP cc_start: 0.8666 (p90) cc_final: 0.8224 (p90) REVERT: U 286 GLU cc_start: 0.8045 (tt0) cc_final: 0.7829 (tt0) REVERT: V 100 ILE cc_start: 0.8839 (mp) cc_final: 0.8613 (mp) REVERT: V 125 GLU cc_start: 0.9076 (pt0) cc_final: 0.8860 (pt0) REVERT: V 158 ASP cc_start: 0.7596 (t0) cc_final: 0.7038 (t70) REVERT: V 182 ASN cc_start: 0.8641 (m110) cc_final: 0.8057 (m-40) REVERT: V 196 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6498 (mt-10) REVERT: V 202 ASP cc_start: 0.7857 (t70) cc_final: 0.7637 (t70) REVERT: V 284 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7631 (m90) REVERT: V 442 LEU cc_start: 0.8434 (mt) cc_final: 0.8054 (mt) REVERT: V 448 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7939 (tp30) REVERT: V 453 LYS cc_start: 0.7417 (ttmt) cc_final: 0.6416 (ttmm) REVERT: X 36 GLU cc_start: 0.8707 (mp0) cc_final: 0.8317 (mp0) REVERT: X 146 TRP cc_start: 0.9096 (p90) cc_final: 0.8841 (p90) REVERT: X 217 TRP cc_start: 0.8922 (p90) cc_final: 0.8405 (p90) REVERT: X 282 GLU cc_start: 0.7319 (tt0) cc_final: 0.6989 (tt0) outliers start: 9 outliers final: 0 residues processed: 2168 average time/residue: 0.6230 time to fit residues: 2291.3304 Evaluate side-chains 1819 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1815 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 715 optimal weight: 0.2980 chunk 753 optimal weight: 2.9990 chunk 687 optimal weight: 2.9990 chunk 732 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 575 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 662 optimal weight: 1.9990 chunk 693 optimal weight: 0.7980 chunk 730 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 284 HIS ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN F 284 HIS ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 HIS ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN L 284 HIS ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 284 HIS ** N 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN ** P 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 ASN R 284 HIS ** R 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 284 HIS ** T 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 69108 Z= 0.236 Angle : 0.560 10.672 93204 Z= 0.298 Chirality : 0.042 0.134 9840 Planarity : 0.004 0.035 12240 Dihedral : 4.491 20.728 9120 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.19 % Allowed : 0.33 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.36 (0.09), residues: 8280 helix: 1.08 (0.09), residues: 3180 sheet: -1.09 (0.15), residues: 1152 loop : 0.11 (0.10), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 312 HIS 0.004 0.001 HIS W 77 PHE 0.019 0.001 PHE J 308 TYR 0.017 0.001 TYR O 294 ARG 0.009 0.001 ARG L 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2134 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 2120 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8909 (mp) cc_final: 0.8696 (mp) REVERT: A 112 CYS cc_start: 0.7472 (t) cc_final: 0.7181 (t) REVERT: A 117 TYR cc_start: 0.7203 (m-80) cc_final: 0.6770 (m-10) REVERT: A 158 ASP cc_start: 0.7423 (t70) cc_final: 0.7107 (t70) REVERT: A 182 ASN cc_start: 0.8634 (m110) cc_final: 0.7806 (m-40) REVERT: A 301 SER cc_start: 0.8919 (m) cc_final: 0.8527 (p) REVERT: A 411 GLU cc_start: 0.8118 (pp20) cc_final: 0.7681 (pp20) REVERT: A 428 PHE cc_start: 0.8798 (t80) cc_final: 0.8497 (t80) REVERT: A 448 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7790 (tp30) REVERT: A 452 PHE cc_start: 0.6651 (t80) cc_final: 0.6102 (t80) REVERT: A 453 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7649 (ttmm) REVERT: A 462 GLN cc_start: 0.7718 (tp40) cc_final: 0.7119 (tt0) REVERT: W 39 ASN cc_start: 0.8289 (m110) cc_final: 0.7900 (m110) REVERT: W 120 ARG cc_start: 0.8737 (mtt90) cc_final: 0.8472 (ttt90) REVERT: W 144 ASN cc_start: 0.8319 (p0) cc_final: 0.8112 (p0) REVERT: W 217 TRP cc_start: 0.8850 (p90) cc_final: 0.8321 (p90) REVERT: B 78 MET cc_start: 0.6738 (mmm) cc_final: 0.6223 (ptm) REVERT: B 144 LYS cc_start: 0.8033 (mttp) cc_final: 0.7831 (mmtp) REVERT: B 145 ARG cc_start: 0.8544 (ptp-110) cc_final: 0.7475 (ptp-110) REVERT: B 224 VAL cc_start: 0.9268 (p) cc_final: 0.9038 (t) REVERT: B 306 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7799 (tm-30) REVERT: B 453 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7523 (tttp) REVERT: B 487 GLN cc_start: 0.6669 (tp40) cc_final: 0.6404 (tm-30) REVERT: C 33 ASP cc_start: 0.7799 (t0) cc_final: 0.7386 (t0) REVERT: C 36 GLU cc_start: 0.8756 (mp0) cc_final: 0.7687 (mp0) REVERT: C 56 MET cc_start: 0.8662 (mtm) cc_final: 0.8383 (mtm) REVERT: C 144 ASN cc_start: 0.8595 (p0) cc_final: 0.8384 (p0) REVERT: C 217 TRP cc_start: 0.8540 (p90) cc_final: 0.8180 (p90) REVERT: C 282 GLU cc_start: 0.7248 (tt0) cc_final: 0.7029 (tt0) REVERT: D 100 ILE cc_start: 0.8913 (mp) cc_final: 0.8673 (mp) REVERT: D 117 TYR cc_start: 0.7515 (m-80) cc_final: 0.6871 (m-80) REVERT: D 158 ASP cc_start: 0.7649 (t0) cc_final: 0.7327 (t70) REVERT: D 182 ASN cc_start: 0.8481 (m110) cc_final: 0.7951 (m-40) REVERT: D 196 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6466 (mt-10) REVERT: D 222 ARG cc_start: 0.9329 (ttt90) cc_final: 0.8867 (tpt-90) REVERT: D 244 ILE cc_start: 0.8718 (mm) cc_final: 0.8507 (pt) REVERT: D 310 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7396 (ttm170) REVERT: D 329 MET cc_start: 0.8673 (mtp) cc_final: 0.8341 (mtt) REVERT: D 359 SER cc_start: 0.9137 (m) cc_final: 0.8906 (m) REVERT: D 442 LEU cc_start: 0.8169 (mt) cc_final: 0.7969 (mt) REVERT: D 453 LYS cc_start: 0.7452 (ttmt) cc_final: 0.6890 (ttmm) REVERT: D 462 GLN cc_start: 0.7463 (tp40) cc_final: 0.7213 (tp40) REVERT: E 36 GLU cc_start: 0.8776 (mp0) cc_final: 0.8379 (mp0) REVERT: E 146 TRP cc_start: 0.9176 (p90) cc_final: 0.8934 (p90) REVERT: E 217 TRP cc_start: 0.8965 (p90) cc_final: 0.8470 (p90) REVERT: E 282 GLU cc_start: 0.7351 (tt0) cc_final: 0.6953 (tt0) REVERT: F 100 ILE cc_start: 0.8924 (mp) cc_final: 0.8717 (mp) REVERT: F 145 ARG cc_start: 0.8219 (ptp-110) cc_final: 0.6923 (ptp-110) REVERT: F 158 ASP cc_start: 0.7404 (t70) cc_final: 0.7169 (t70) REVERT: F 160 ASP cc_start: 0.7926 (m-30) cc_final: 0.7590 (m-30) REVERT: F 182 ASN cc_start: 0.8660 (m110) cc_final: 0.7802 (m-40) REVERT: F 300 GLN cc_start: 0.7779 (mp10) cc_final: 0.7439 (mp10) REVERT: F 329 MET cc_start: 0.8537 (mtt) cc_final: 0.8325 (mtt) REVERT: F 411 GLU cc_start: 0.8106 (pp20) cc_final: 0.7730 (pp20) REVERT: F 448 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7815 (tp30) REVERT: F 452 PHE cc_start: 0.6612 (t80) cc_final: 0.6133 (t80) REVERT: F 453 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7705 (ttmm) REVERT: G 36 GLU cc_start: 0.8780 (mp0) cc_final: 0.8362 (mp0) REVERT: G 144 ASN cc_start: 0.8361 (p0) cc_final: 0.8116 (p0) REVERT: G 217 TRP cc_start: 0.8829 (p90) cc_final: 0.8326 (p90) REVERT: G 282 GLU cc_start: 0.7217 (tt0) cc_final: 0.6990 (tt0) REVERT: H 78 MET cc_start: 0.6729 (mmm) cc_final: 0.6223 (ptm) REVERT: H 117 TYR cc_start: 0.6944 (m-80) cc_final: 0.6343 (m-80) REVERT: H 143 MET cc_start: 0.7398 (mtm) cc_final: 0.7192 (mmm) REVERT: H 144 LYS cc_start: 0.7931 (mttp) cc_final: 0.7729 (tppt) REVERT: H 145 ARG cc_start: 0.8600 (ptp-110) cc_final: 0.7521 (ptp-110) REVERT: H 182 ASN cc_start: 0.8669 (m110) cc_final: 0.7364 (m-40) REVERT: H 239 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6837 (mt-10) REVERT: H 306 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7701 (tm-30) REVERT: H 453 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7603 (tttp) REVERT: H 487 GLN cc_start: 0.6677 (tp40) cc_final: 0.6405 (tm-30) REVERT: I 56 MET cc_start: 0.8638 (mtm) cc_final: 0.8374 (mtm) REVERT: I 149 GLU cc_start: 0.7986 (mp0) cc_final: 0.7650 (mt-10) REVERT: I 217 TRP cc_start: 0.8511 (p90) cc_final: 0.8135 (p90) REVERT: J 100 ILE cc_start: 0.8905 (mp) cc_final: 0.8670 (mp) REVERT: J 117 TYR cc_start: 0.7515 (m-80) cc_final: 0.6865 (m-80) REVERT: J 158 ASP cc_start: 0.7693 (t0) cc_final: 0.7312 (t70) REVERT: J 182 ASN cc_start: 0.8607 (m110) cc_final: 0.8002 (m-40) REVERT: J 196 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6482 (mt-10) REVERT: J 202 ASP cc_start: 0.7877 (t70) cc_final: 0.7665 (t70) REVERT: J 222 ARG cc_start: 0.9323 (ttt90) cc_final: 0.8758 (tpt-90) REVERT: J 306 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7874 (tm-30) REVERT: J 329 MET cc_start: 0.8641 (mtm) cc_final: 0.8432 (mtt) REVERT: J 359 SER cc_start: 0.9146 (m) cc_final: 0.8929 (m) REVERT: J 448 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7776 (tm-30) REVERT: J 453 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7100 (tttp) REVERT: K 36 GLU cc_start: 0.8779 (mp0) cc_final: 0.8398 (mp0) REVERT: K 146 TRP cc_start: 0.9184 (p90) cc_final: 0.8926 (p90) REVERT: K 217 TRP cc_start: 0.8917 (p90) cc_final: 0.8419 (p90) REVERT: K 282 GLU cc_start: 0.7348 (tt0) cc_final: 0.7000 (tt0) REVERT: L 100 ILE cc_start: 0.8921 (mp) cc_final: 0.8714 (mp) REVERT: L 112 CYS cc_start: 0.7398 (t) cc_final: 0.7072 (t) REVERT: L 160 ASP cc_start: 0.7945 (m-30) cc_final: 0.7549 (m-30) REVERT: L 182 ASN cc_start: 0.8663 (m110) cc_final: 0.7820 (m-40) REVERT: L 329 MET cc_start: 0.8506 (mtm) cc_final: 0.8243 (mtt) REVERT: L 448 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7799 (tp30) REVERT: L 452 PHE cc_start: 0.6615 (t80) cc_final: 0.6123 (t80) REVERT: L 453 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7697 (ttmm) REVERT: M 36 GLU cc_start: 0.8775 (mp0) cc_final: 0.8354 (mp0) REVERT: M 144 ASN cc_start: 0.8341 (p0) cc_final: 0.8099 (p0) REVERT: M 217 TRP cc_start: 0.8865 (p90) cc_final: 0.8275 (p90) REVERT: M 282 GLU cc_start: 0.7251 (tt0) cc_final: 0.7010 (tt0) REVERT: M 297 TYR cc_start: 0.7480 (m-80) cc_final: 0.7195 (m-10) REVERT: N 78 MET cc_start: 0.6711 (mmm) cc_final: 0.6211 (ptm) REVERT: N 117 TYR cc_start: 0.7335 (m-80) cc_final: 0.6995 (m-80) REVERT: N 145 ARG cc_start: 0.8559 (ptp-110) cc_final: 0.7500 (ptp-110) REVERT: N 182 ASN cc_start: 0.8564 (m110) cc_final: 0.7541 (m-40) REVERT: N 224 VAL cc_start: 0.9283 (p) cc_final: 0.8995 (t) REVERT: N 300 GLN cc_start: 0.7624 (mp10) cc_final: 0.7329 (mt0) REVERT: N 306 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7708 (tm-30) REVERT: N 453 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7544 (tttp) REVERT: N 487 GLN cc_start: 0.6663 (tp40) cc_final: 0.6435 (tm-30) REVERT: O 33 ASP cc_start: 0.7806 (t0) cc_final: 0.7386 (t0) REVERT: O 36 GLU cc_start: 0.8755 (mp0) cc_final: 0.7685 (mp0) REVERT: O 56 MET cc_start: 0.8646 (mtm) cc_final: 0.8379 (mtm) REVERT: O 120 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8372 (ttt90) REVERT: O 217 TRP cc_start: 0.8552 (p90) cc_final: 0.8177 (p90) REVERT: P 100 ILE cc_start: 0.8902 (mp) cc_final: 0.8672 (mp) REVERT: P 117 TYR cc_start: 0.7477 (m-80) cc_final: 0.6838 (m-80) REVERT: P 125 GLU cc_start: 0.8755 (tt0) cc_final: 0.8365 (pt0) REVERT: P 158 ASP cc_start: 0.7650 (t0) cc_final: 0.7298 (t70) REVERT: P 182 ASN cc_start: 0.8614 (m110) cc_final: 0.8007 (m-40) REVERT: P 196 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6492 (mt-10) REVERT: P 202 ASP cc_start: 0.7877 (t70) cc_final: 0.7670 (t70) REVERT: P 222 ARG cc_start: 0.9307 (ttt90) cc_final: 0.8894 (tpt-90) REVERT: P 359 SER cc_start: 0.9149 (m) cc_final: 0.8939 (m) REVERT: P 446 LYS cc_start: 0.7839 (tttt) cc_final: 0.7631 (pttp) REVERT: P 448 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7772 (tm-30) REVERT: P 453 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7125 (tttp) REVERT: Q 36 GLU cc_start: 0.8685 (mp0) cc_final: 0.8319 (mp0) REVERT: Q 146 TRP cc_start: 0.9181 (p90) cc_final: 0.8929 (p90) REVERT: Q 217 TRP cc_start: 0.8956 (p90) cc_final: 0.8399 (p90) REVERT: Q 254 GLU cc_start: 0.6779 (tt0) cc_final: 0.6561 (tt0) REVERT: Q 282 GLU cc_start: 0.7386 (tt0) cc_final: 0.7055 (tt0) REVERT: R 100 ILE cc_start: 0.8921 (mp) cc_final: 0.8684 (mp) REVERT: R 112 CYS cc_start: 0.7568 (t) cc_final: 0.7232 (t) REVERT: R 158 ASP cc_start: 0.7377 (t0) cc_final: 0.7137 (t70) REVERT: R 160 ASP cc_start: 0.7873 (m-30) cc_final: 0.7646 (m-30) REVERT: R 182 ASN cc_start: 0.8754 (m110) cc_final: 0.8004 (m-40) REVERT: R 300 GLN cc_start: 0.7730 (mp10) cc_final: 0.7279 (mp10) REVERT: R 329 MET cc_start: 0.8495 (mtt) cc_final: 0.8259 (mtt) REVERT: R 411 GLU cc_start: 0.8145 (pp20) cc_final: 0.7705 (pp20) REVERT: R 428 PHE cc_start: 0.8789 (t80) cc_final: 0.8479 (t80) REVERT: R 452 PHE cc_start: 0.6740 (t80) cc_final: 0.6320 (t80) REVERT: R 453 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7801 (ttmm) REVERT: S 36 GLU cc_start: 0.8770 (mp0) cc_final: 0.8361 (mp0) REVERT: S 120 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8512 (ttt90) REVERT: S 144 ASN cc_start: 0.8360 (p0) cc_final: 0.8118 (p0) REVERT: S 217 TRP cc_start: 0.8862 (p90) cc_final: 0.8327 (p90) REVERT: S 297 TYR cc_start: 0.7441 (m-80) cc_final: 0.7132 (m-10) REVERT: T 145 ARG cc_start: 0.8548 (ptp-110) cc_final: 0.7504 (ptp-110) REVERT: T 182 ASN cc_start: 0.8590 (m110) cc_final: 0.7609 (m-40) REVERT: T 224 VAL cc_start: 0.9297 (p) cc_final: 0.9008 (t) REVERT: T 300 GLN cc_start: 0.7622 (mp10) cc_final: 0.7385 (mt0) REVERT: T 445 LEU cc_start: 0.8501 (tp) cc_final: 0.8281 (tp) REVERT: T 453 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7566 (tttp) REVERT: T 487 GLN cc_start: 0.6672 (tp40) cc_final: 0.6409 (tm-30) REVERT: U 33 ASP cc_start: 0.7801 (t0) cc_final: 0.7380 (t0) REVERT: U 36 GLU cc_start: 0.8698 (mp0) cc_final: 0.7744 (mp0) REVERT: U 56 MET cc_start: 0.8648 (mtm) cc_final: 0.8366 (mtm) REVERT: U 217 TRP cc_start: 0.8609 (p90) cc_final: 0.8186 (p90) REVERT: U 222 GLU cc_start: 0.8295 (mp0) cc_final: 0.8076 (mp0) REVERT: V 100 ILE cc_start: 0.8900 (mp) cc_final: 0.8682 (mp) REVERT: V 117 TYR cc_start: 0.7445 (m-80) cc_final: 0.6807 (m-80) REVERT: V 129 ARG cc_start: 0.7252 (tpt-90) cc_final: 0.6926 (tpt-90) REVERT: V 158 ASP cc_start: 0.7599 (t0) cc_final: 0.7220 (t70) REVERT: V 182 ASN cc_start: 0.8594 (m110) cc_final: 0.7988 (m-40) REVERT: V 196 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6499 (mt-10) REVERT: V 222 ARG cc_start: 0.9322 (ttt90) cc_final: 0.9013 (ttm-80) REVERT: V 359 SER cc_start: 0.9128 (m) cc_final: 0.8920 (m) REVERT: V 442 LEU cc_start: 0.8236 (mt) cc_final: 0.8001 (mt) REVERT: V 453 LYS cc_start: 0.7402 (ttmt) cc_final: 0.6378 (ttmm) REVERT: X 36 GLU cc_start: 0.8688 (mp0) cc_final: 0.8335 (mp0) REVERT: X 146 TRP cc_start: 0.9153 (p90) cc_final: 0.8900 (p90) REVERT: X 217 TRP cc_start: 0.8965 (p90) cc_final: 0.8465 (p90) REVERT: X 282 GLU cc_start: 0.7379 (tt0) cc_final: 0.7036 (tt0) outliers start: 14 outliers final: 9 residues processed: 2126 average time/residue: 0.6256 time to fit residues: 2254.8916 Evaluate side-chains 1813 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1804 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 481 optimal weight: 1.9990 chunk 775 optimal weight: 0.1980 chunk 473 optimal weight: 0.7980 chunk 367 optimal weight: 0.5980 chunk 538 optimal weight: 1.9990 chunk 812 optimal weight: 4.9990 chunk 748 optimal weight: 7.9990 chunk 647 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 500 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 HIS ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN P 284 HIS ** P 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 ASN ** R 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 HIS ** V 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 69108 Z= 0.184 Angle : 0.534 10.118 93204 Z= 0.286 Chirality : 0.041 0.157 9840 Planarity : 0.004 0.036 12240 Dihedral : 4.414 20.864 9120 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.12 % Allowed : 0.15 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.42 (0.09), residues: 8280 helix: 1.12 (0.09), residues: 3204 sheet: -1.05 (0.15), residues: 1152 loop : 0.14 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 312 HIS 0.005 0.001 HIS W 77 PHE 0.022 0.001 PHE C 133 TYR 0.034 0.001 TYR L 117 ARG 0.009 0.001 ARG D 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16560 Ramachandran restraints generated. 8280 Oldfield, 0 Emsley, 8280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2133 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2124 time to evaluate : 5.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6989 (mmp) cc_final: 0.6564 (mtp) REVERT: A 100 ILE cc_start: 0.8898 (mp) cc_final: 0.8664 (mp) REVERT: A 112 CYS cc_start: 0.7455 (t) cc_final: 0.7111 (t) REVERT: A 158 ASP cc_start: 0.7367 (t70) cc_final: 0.7148 (t70) REVERT: A 176 TYR cc_start: 0.8479 (m-10) cc_final: 0.8022 (m-10) REVERT: A 182 ASN cc_start: 0.8669 (m110) cc_final: 0.7966 (m-40) REVERT: A 249 THR cc_start: 0.8754 (p) cc_final: 0.8507 (p) REVERT: A 411 GLU cc_start: 0.8057 (pp20) cc_final: 0.7492 (pp20) REVERT: A 448 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7773 (tp30) REVERT: A 452 PHE cc_start: 0.6679 (t80) cc_final: 0.6021 (t80) REVERT: A 453 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7606 (ttmm) REVERT: A 462 GLN cc_start: 0.7596 (tp40) cc_final: 0.7087 (tt0) REVERT: W 120 ARG cc_start: 0.8698 (mtt90) cc_final: 0.8472 (ttt90) REVERT: W 144 ASN cc_start: 0.8312 (p0) cc_final: 0.8093 (p0) REVERT: W 217 TRP cc_start: 0.8842 (p90) cc_final: 0.8311 (p90) REVERT: B 78 MET cc_start: 0.6838 (mmm) cc_final: 0.6261 (ptm) REVERT: B 144 LYS cc_start: 0.8031 (mttp) cc_final: 0.7775 (tppt) REVERT: B 145 ARG cc_start: 0.8530 (ptp-110) cc_final: 0.7449 (ptp-110) REVERT: B 202 ASP cc_start: 0.7973 (t70) cc_final: 0.7488 (t0) REVERT: B 224 VAL cc_start: 0.9290 (p) cc_final: 0.9076 (m) REVERT: B 248 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8274 (ttp80) REVERT: B 306 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7754 (tm-30) REVERT: B 453 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7502 (tttp) REVERT: C 33 ASP cc_start: 0.7784 (t0) cc_final: 0.7390 (t0) REVERT: C 36 GLU cc_start: 0.8709 (mp0) cc_final: 0.7584 (mp0) REVERT: C 40 LEU cc_start: 0.8469 (mt) cc_final: 0.8040 (mt) REVERT: C 56 MET cc_start: 0.8617 (mtm) cc_final: 0.8329 (mtm) REVERT: C 217 TRP cc_start: 0.8703 (p90) cc_final: 0.8237 (p90) REVERT: C 219 MET cc_start: 0.8641 (ttm) cc_final: 0.8424 (ttm) REVERT: C 282 GLU cc_start: 0.7215 (tt0) cc_final: 0.6992 (tt0) REVERT: D 100 ILE cc_start: 0.8931 (mp) cc_final: 0.8690 (mp) REVERT: D 158 ASP cc_start: 0.7699 (t0) cc_final: 0.7326 (t70) REVERT: D 182 ASN cc_start: 0.8443 (m110) cc_final: 0.7954 (m-40) REVERT: D 196 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6443 (mt-10) REVERT: D 222 ARG cc_start: 0.9311 (ttt90) cc_final: 0.8899 (tpt-90) REVERT: D 244 ILE cc_start: 0.8701 (mm) cc_final: 0.8453 (pt) REVERT: D 284 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7581 (m90) REVERT: D 329 MET cc_start: 0.8634 (mtp) cc_final: 0.8305 (mtm) REVERT: D 442 LEU cc_start: 0.8393 (mt) cc_final: 0.7973 (mt) REVERT: D 446 LYS cc_start: 0.8165 (pttm) cc_final: 0.7958 (pttm) REVERT: D 453 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6847 (ttmm) REVERT: E 36 GLU cc_start: 0.8784 (mp0) cc_final: 0.8372 (mp0) REVERT: E 146 TRP cc_start: 0.9104 (p90) cc_final: 0.8850 (p90) REVERT: E 217 TRP cc_start: 0.8932 (p90) cc_final: 0.8508 (p90) REVERT: E 282 GLU cc_start: 0.7364 (tt0) cc_final: 0.7055 (tt0) REVERT: F 100 ILE cc_start: 0.8932 (mp) cc_final: 0.8696 (mp) REVERT: F 145 ARG cc_start: 0.8235 (ptp-110) cc_final: 0.6991 (ptp-110) REVERT: F 161 ARG cc_start: 0.7406 (ttp80) cc_final: 0.6699 (ttp-170) REVERT: F 182 ASN cc_start: 0.8720 (m110) cc_final: 0.7963 (m-40) REVERT: F 329 MET cc_start: 0.8534 (mtt) cc_final: 0.8229 (mtt) REVERT: F 448 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7795 (tp30) REVERT: F 452 PHE cc_start: 0.6614 (t80) cc_final: 0.6103 (t80) REVERT: F 453 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7672 (ttmm) REVERT: F 462 GLN cc_start: 0.7871 (tp40) cc_final: 0.7535 (tp40) REVERT: G 36 GLU cc_start: 0.8828 (mp0) cc_final: 0.8393 (mp0) REVERT: G 129 LEU cc_start: 0.9111 (tp) cc_final: 0.8908 (tp) REVERT: G 144 ASN cc_start: 0.8312 (p0) cc_final: 0.8076 (p0) REVERT: G 217 TRP cc_start: 0.8824 (p90) cc_final: 0.8287 (p90) REVERT: H 78 MET cc_start: 0.6824 (mmm) cc_final: 0.6261 (ptm) REVERT: H 143 MET cc_start: 0.7387 (mtm) cc_final: 0.7184 (mmm) REVERT: H 145 ARG cc_start: 0.8541 (ptp-110) cc_final: 0.7429 (ptp-110) REVERT: H 182 ASN cc_start: 0.8643 (m110) cc_final: 0.7422 (m-40) REVERT: H 306 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7649 (tm-30) REVERT: H 453 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7600 (tttp) REVERT: I 56 MET cc_start: 0.8603 (mtm) cc_final: 0.8328 (mtm) REVERT: I 149 GLU cc_start: 0.7925 (mp0) cc_final: 0.7467 (mt-10) REVERT: I 217 TRP cc_start: 0.8614 (p90) cc_final: 0.8228 (p90) REVERT: J 100 ILE cc_start: 0.8926 (mp) cc_final: 0.8672 (mp) REVERT: J 158 ASP cc_start: 0.7744 (t0) cc_final: 0.7273 (t70) REVERT: J 182 ASN cc_start: 0.8543 (m110) cc_final: 0.7920 (m-40) REVERT: J 196 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6464 (mt-10) REVERT: J 222 ARG cc_start: 0.9305 (ttt90) cc_final: 0.8873 (tpt-90) REVERT: J 284 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (m90) REVERT: J 359 SER cc_start: 0.9130 (m) cc_final: 0.8925 (m) REVERT: J 446 LYS cc_start: 0.7864 (tttt) cc_final: 0.7590 (pttp) REVERT: J 448 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7816 (tm-30) REVERT: J 453 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7033 (tttp) REVERT: K 36 GLU cc_start: 0.8797 (mp0) cc_final: 0.8382 (mp0) REVERT: K 146 TRP cc_start: 0.9112 (p90) cc_final: 0.8850 (p90) REVERT: K 217 TRP cc_start: 0.8910 (p90) cc_final: 0.8396 (p90) REVERT: K 282 GLU cc_start: 0.7361 (tt0) cc_final: 0.7127 (tt0) REVERT: L 100 ILE cc_start: 0.8933 (mp) cc_final: 0.8691 (mp) REVERT: L 158 ASP cc_start: 0.7485 (t70) cc_final: 0.7144 (t70) REVERT: L 160 ASP cc_start: 0.7889 (m-30) cc_final: 0.7686 (m-30) REVERT: L 182 ASN cc_start: 0.8733 (m110) cc_final: 0.8005 (m-40) REVERT: L 329 MET cc_start: 0.8474 (mtm) cc_final: 0.8189 (mtt) REVERT: L 359 SER cc_start: 0.9107 (m) cc_final: 0.8896 (m) REVERT: L 448 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7798 (tp30) REVERT: L 452 PHE cc_start: 0.6619 (t80) cc_final: 0.6096 (t80) REVERT: L 453 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7678 (ttmm) REVERT: M 36 GLU cc_start: 0.8825 (mp0) cc_final: 0.8378 (mp0) REVERT: M 144 ASN cc_start: 0.8292 (p0) cc_final: 0.8055 (p0) REVERT: M 217 TRP cc_start: 0.8845 (p90) cc_final: 0.8351 (p90) REVERT: M 282 GLU cc_start: 0.7261 (tt0) cc_final: 0.7027 (tt0) REVERT: N 78 MET cc_start: 0.6817 (mmm) cc_final: 0.6262 (ptm) REVERT: N 117 TYR cc_start: 0.7570 (m-80) cc_final: 0.7341 (m-80) REVERT: N 145 ARG cc_start: 0.8562 (ptp-110) cc_final: 0.7476 (ptp-110) REVERT: N 161 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6613 (ttp-170) REVERT: N 182 ASN cc_start: 0.8649 (m110) cc_final: 0.7499 (m-40) REVERT: N 224 VAL cc_start: 0.9292 (p) cc_final: 0.9025 (m) REVERT: N 453 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7522 (tttp) REVERT: O 33 ASP cc_start: 0.7774 (t0) cc_final: 0.7364 (t0) REVERT: O 36 GLU cc_start: 0.8712 (mp0) cc_final: 0.7584 (mp0) REVERT: O 40 LEU cc_start: 0.8491 (mt) cc_final: 0.8068 (mt) REVERT: O 56 MET cc_start: 0.8610 (mtm) cc_final: 0.8342 (mtm) REVERT: O 149 GLU cc_start: 0.7975 (mp0) cc_final: 0.7417 (mp0) REVERT: O 217 TRP cc_start: 0.8661 (p90) cc_final: 0.8239 (p90) REVERT: P 100 ILE cc_start: 0.8928 (mp) cc_final: 0.8675 (mp) REVERT: P 125 GLU cc_start: 0.8704 (tt0) cc_final: 0.8312 (pt0) REVERT: P 158 ASP cc_start: 0.7704 (t0) cc_final: 0.7282 (t70) REVERT: P 182 ASN cc_start: 0.8569 (m110) cc_final: 0.7939 (m-40) REVERT: P 196 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6464 (mt-10) REVERT: P 222 ARG cc_start: 0.9292 (ttt90) cc_final: 0.8922 (tpt-90) REVERT: P 284 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7583 (m90) REVERT: P 359 SER cc_start: 0.9132 (m) cc_final: 0.8928 (m) REVERT: P 448 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7807 (tm-30) REVERT: P 453 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7040 (tttp) REVERT: Q 36 GLU cc_start: 0.8674 (mp0) cc_final: 0.8351 (mp0) REVERT: Q 146 TRP cc_start: 0.9116 (p90) cc_final: 0.8856 (p90) REVERT: Q 217 TRP cc_start: 0.8906 (p90) cc_final: 0.8362 (p90) REVERT: Q 282 GLU cc_start: 0.7389 (tt0) cc_final: 0.7132 (tt0) REVERT: R 100 ILE cc_start: 0.8923 (mp) cc_final: 0.8692 (mp) REVERT: R 112 CYS cc_start: 0.7422 (t) cc_final: 0.7049 (t) REVERT: R 161 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6637 (ttp-170) REVERT: R 182 ASN cc_start: 0.8612 (m110) cc_final: 0.7914 (m-40) REVERT: R 329 MET cc_start: 0.8470 (mtt) cc_final: 0.8194 (mtt) REVERT: R 411 GLU cc_start: 0.8194 (pp20) cc_final: 0.7667 (pp20) REVERT: R 448 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7749 (tp30) REVERT: R 452 PHE cc_start: 0.6752 (t80) cc_final: 0.6113 (t80) REVERT: R 453 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7700 (ttmm) REVERT: S 36 GLU cc_start: 0.8817 (mp0) cc_final: 0.8394 (mp0) REVERT: S 217 TRP cc_start: 0.8840 (p90) cc_final: 0.8352 (p90) REVERT: T 145 ARG cc_start: 0.8524 (ptp-110) cc_final: 0.7428 (ptp-110) REVERT: T 224 VAL cc_start: 0.9286 (p) cc_final: 0.9055 (m) REVERT: T 229 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7662 (mtmt) REVERT: T 453 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7526 (tttp) REVERT: U 33 ASP cc_start: 0.7795 (t0) cc_final: 0.7417 (t0) REVERT: U 36 GLU cc_start: 0.8708 (mp0) cc_final: 0.7669 (mp0) REVERT: U 56 MET cc_start: 0.8590 (mtm) cc_final: 0.8321 (mtm) REVERT: U 134 ASN cc_start: 0.8712 (p0) cc_final: 0.8384 (p0) REVERT: U 217 TRP cc_start: 0.8598 (p90) cc_final: 0.8268 (p90) REVERT: V 100 ILE cc_start: 0.8926 (mp) cc_final: 0.8698 (mp) REVERT: V 158 ASP cc_start: 0.7723 (t0) cc_final: 0.7106 (t70) REVERT: V 182 ASN cc_start: 0.8528 (m110) cc_final: 0.7947 (m-40) REVERT: V 196 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6445 (mt-10) REVERT: V 222 ARG cc_start: 0.9294 (ttt90) cc_final: 0.9016 (ttm-80) REVERT: V 284 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7613 (m90) REVERT: V 359 SER cc_start: 0.9092 (m) cc_final: 0.8860 (m) REVERT: V 442 LEU cc_start: 0.8412 (mt) cc_final: 0.8019 (mt) REVERT: V 453 LYS cc_start: 0.7363 (ttmt) cc_final: 0.6337 (ttmm) REVERT: V 462 GLN cc_start: 0.7539 (tp40) cc_final: 0.7266 (tp40) REVERT: X 36 GLU cc_start: 0.8688 (mp0) cc_final: 0.8354 (mp0) REVERT: X 146 TRP cc_start: 0.9089 (p90) cc_final: 0.8840 (p90) REVERT: X 217 TRP cc_start: 0.8923 (p90) cc_final: 0.8407 (p90) REVERT: X 282 GLU cc_start: 0.7370 (tt0) cc_final: 0.7110 (tt0) outliers start: 9 outliers final: 2 residues processed: 2129 average time/residue: 0.6473 time to fit residues: 2350.4759 Evaluate side-chains 1821 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1815 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 816 random chunks: chunk 514 optimal weight: 1.9990 chunk 689 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 596 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 179 optimal weight: 0.0000 chunk 648 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 665 optimal weight: 2.9990 chunk 82 optimal weight: 0.0050 chunk 119 optimal weight: 2.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN F 284 HIS ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 GLN H 284 HIS ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 ASN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 ASN L 284 HIS ** L 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 284 HIS N 417 HIS ** N 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 144 ASN O 214 ASN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 ASN R 284 HIS ** R 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 284 HIS ** T 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.145548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.120040 restraints weight = 97555.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.122690 restraints weight = 65184.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.124622 restraints weight = 46911.047| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 69108 Z= 0.177 Angle : 0.538 9.899 93204 Z= 0.287 Chirality : 0.041 0.137 9840 Planarity : 0.004 0.036 12240 Dihedral : 4.347 24.519 9120 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.21 % Allowed : 0.28 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.45 (0.09), residues: 8280 helix: 1.18 (0.09), residues: 3204 sheet: -1.01 (0.15), residues: 1152 loop : 0.12 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 312 HIS 0.006 0.001 HIS C 154 PHE 0.017 0.001 PHE D 308 TYR 0.035 0.001 TYR P 117 ARG 0.009 0.001 ARG J 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28283.30 seconds wall clock time: 487 minutes 53.03 seconds (29273.03 seconds total)