Starting phenix.real_space_refine on Tue Aug 26 15:20:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt4_19478/08_2025/8rt4_19478.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt4_19478/08_2025/8rt4_19478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rt4_19478/08_2025/8rt4_19478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt4_19478/08_2025/8rt4_19478.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt4_19478/08_2025/8rt4_19478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt4_19478/08_2025/8rt4_19478.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.068 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 23996 2.51 5 N 6972 2.21 5 O 7350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 280 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38458 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: D, G, J, M, P, S, V, Y, b, e, h, k, n, E, H, K, N, Q, T, W, Z, c, f, i, l, o, F, I, L, O, R, U, X, a, d, g, j, m, p Time building chain proxies: 4.21, per 1000 atoms: 0.11 Number of scatterers: 38458 At special positions: 0 Unit cell: (193.127, 195.261, 100.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 7350 8.00 N 6972 7.00 C 23996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS M 215 " - pdb=" SG CYS M 231 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 231 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 231 " distance=2.03 Simple disulfide: pdb=" SG CYS V 215 " - pdb=" SG CYS V 231 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 215 " - pdb=" SG CYS Y 231 " distance=2.03 Simple disulfide: pdb=" SG CYS b 215 " - pdb=" SG CYS b 231 " distance=2.03 Simple disulfide: pdb=" SG CYS e 215 " - pdb=" SG CYS e 231 " distance=2.03 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.03 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9016 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 112 sheets defined 17.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'D' and resid 180 through 187 Processing helix chain 'D' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.509A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 151 removed outlier: 4.068A pdb=" N ARG H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 169 Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.509A pdb=" N ASN J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 151 removed outlier: 4.068A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'M' and resid 180 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA M 313 " --> pdb=" O ARG M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN M 357 " --> pdb=" O GLU M 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG N 151 " --> pdb=" O ALA N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 169 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN P 357 " --> pdb=" O GLU P 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 151 removed outlier: 4.067A pdb=" N ARG Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 169 Processing helix chain 'S' and resid 180 through 187 Processing helix chain 'S' and resid 305 through 329 removed outlier: 5.603A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 169 Processing helix chain 'V' and resid 180 through 187 Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA V 313 " --> pdb=" O ARG V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN V 357 " --> pdb=" O GLU V 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG W 151 " --> pdb=" O ALA W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 169 Processing helix chain 'Y' and resid 180 through 187 Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.603A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA Y 313 " --> pdb=" O ARG Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN Y 357 " --> pdb=" O GLU Y 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG Z 151 " --> pdb=" O ALA Z 147 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 removed outlier: 3.509A pdb=" N ASN b 357 " --> pdb=" O GLU b 353 " (cutoff:3.500A) Processing helix chain 'c' and resid 137 through 151 removed outlier: 4.070A pdb=" N ARG c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 169 Processing helix chain 'e' and resid 180 through 187 Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.511A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 151 removed outlier: 4.071A pdb=" N ARG f 151 " --> pdb=" O ALA f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 169 Processing helix chain 'h' and resid 180 through 187 Processing helix chain 'h' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN h 357 " --> pdb=" O GLU h 353 " (cutoff:3.500A) Processing helix chain 'i' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 169 Processing helix chain 'k' and resid 180 through 187 Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN k 357 " --> pdb=" O GLU k 353 " (cutoff:3.500A) Processing helix chain 'l' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'n' and resid 180 through 187 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 removed outlier: 3.508A pdb=" N ASN n 357 " --> pdb=" O GLU n 353 " (cutoff:3.500A) Processing helix chain 'o' and resid 137 through 151 removed outlier: 4.068A pdb=" N ARG o 151 " --> pdb=" O ALA o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.771A pdb=" N SER A 195 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL D 270 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS D 252 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE D 275 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D 254 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA4, first strand: chain 'n' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL A 270 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 252 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 275 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 254 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 391 Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AB3, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.776A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL G 270 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS G 252 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE G 275 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL G 254 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AB7, first strand: chain 'D' and resid 267 through 268 Processing sheet with id=AB8, first strand: chain 'D' and resid 387 through 391 Processing sheet with id=AB9, first strand: chain 'E' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AC2, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.743A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL J 270 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC5, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AC6, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AC7, first strand: chain 'G' and resid 387 through 391 Processing sheet with id=AC8, first strand: chain 'H' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AD1, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.754A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 198 through 199 removed outlier: 4.829A pdb=" N VAL M 270 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS M 252 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE M 275 " --> pdb=" O LYS M 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL M 254 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AD4, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=AD5, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AD6, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AD7, first strand: chain 'K' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AD9, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.770A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL P 270 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AE3, first strand: chain 'M' and resid 237 through 238 Processing sheet with id=AE4, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AE5, first strand: chain 'M' and resid 387 through 391 Processing sheet with id=AE6, first strand: chain 'N' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 172 through 175 Processing sheet with id=AE8, first strand: chain 'P' and resid 195 through 196 removed outlier: 6.772A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'P' and resid 237 through 238 Processing sheet with id=AF3, first strand: chain 'P' and resid 267 through 268 Processing sheet with id=AF4, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AF5, first strand: chain 'Q' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 172 through 175 Processing sheet with id=AF7, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.765A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL V 270 " --> pdb=" O GLY V 289 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AG1, first strand: chain 'S' and resid 237 through 238 Processing sheet with id=AG2, first strand: chain 'S' and resid 267 through 268 Processing sheet with id=AG3, first strand: chain 'S' and resid 387 through 391 Processing sheet with id=AG4, first strand: chain 'T' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 172 through 175 Processing sheet with id=AG6, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.759A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL Y 270 " --> pdb=" O GLY Y 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AG9, first strand: chain 'V' and resid 237 through 238 Processing sheet with id=AH1, first strand: chain 'V' and resid 267 through 268 Processing sheet with id=AH2, first strand: chain 'V' and resid 387 through 391 Processing sheet with id=AH3, first strand: chain 'W' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AH5, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.774A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL b 270 " --> pdb=" O GLY b 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS b 252 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE b 275 " --> pdb=" O LYS b 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL b 254 " --> pdb=" O SER b 273 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 221 through 222 Processing sheet with id=AH8, first strand: chain 'Y' and resid 237 through 238 Processing sheet with id=AH9, first strand: chain 'Y' and resid 267 through 268 Processing sheet with id=AI1, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AI2, first strand: chain 'Z' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AI4, first strand: chain 'b' and resid 195 through 196 removed outlier: 6.764A pdb=" N SER b 195 " --> pdb=" O ASP e 382 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'b' and resid 198 through 199 removed outlier: 4.829A pdb=" N VAL e 270 " --> pdb=" O GLY e 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS e 252 " --> pdb=" O ILE e 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE e 275 " --> pdb=" O LYS e 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL e 254 " --> pdb=" O SER e 273 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AI7, first strand: chain 'b' and resid 237 through 238 Processing sheet with id=AI8, first strand: chain 'b' and resid 267 through 268 Processing sheet with id=AI9, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AJ1, first strand: chain 'c' and resid 202 through 203 removed outlier: 4.714A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'c' and resid 172 through 175 Processing sheet with id=AJ3, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.759A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'e' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL h 270 " --> pdb=" O GLY h 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS h 252 " --> pdb=" O ILE h 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE h 275 " --> pdb=" O LYS h 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL h 254 " --> pdb=" O SER h 273 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AJ6, first strand: chain 'e' and resid 237 through 238 Processing sheet with id=AJ7, first strand: chain 'e' and resid 267 through 268 Processing sheet with id=AJ8, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AJ9, first strand: chain 'f' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AK2, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.762A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'h' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL k 270 " --> pdb=" O GLY k 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AK5, first strand: chain 'h' and resid 237 through 238 Processing sheet with id=AK6, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AK7, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AK8, first strand: chain 'i' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AL1, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.772A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'k' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL n 270 " --> pdb=" O GLY n 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AL4, first strand: chain 'k' and resid 237 through 238 Processing sheet with id=AL5, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AL6, first strand: chain 'k' and resid 387 through 391 Processing sheet with id=AL7, first strand: chain 'l' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AL9, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AM1, first strand: chain 'n' and resid 237 through 238 Processing sheet with id=AM2, first strand: chain 'n' and resid 267 through 268 Processing sheet with id=AM3, first strand: chain 'o' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'o' and resid 172 through 175 1555 hydrogen bonds defined for protein. 3993 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: 11.64 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13230 1.34 - 1.45: 6589 1.45 - 1.57: 19143 1.57 - 1.69: 0 1.69 - 1.81: 238 Bond restraints: 39200 Sorted by residual: bond pdb=" CA ARG Q 259 " pdb=" CB ARG Q 259 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.58e-02 4.01e+03 3.60e+00 bond pdb=" CA ARG B 259 " pdb=" CB ARG B 259 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.58e-02 4.01e+03 3.50e+00 bond pdb=" CA ARG l 259 " pdb=" CB ARG l 259 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.58e-02 4.01e+03 3.37e+00 bond pdb=" CA ARG E 259 " pdb=" CB ARG E 259 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.58e-02 4.01e+03 3.35e+00 bond pdb=" CA ARG T 259 " pdb=" CB ARG T 259 " ideal model delta sigma weight residual 1.529 1.557 -0.028 1.58e-02 4.01e+03 3.22e+00 ... (remaining 39195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 51054 1.51 - 3.02: 1732 3.02 - 4.53: 288 4.53 - 6.04: 14 6.04 - 7.55: 42 Bond angle restraints: 53130 Sorted by residual: angle pdb=" N ARG l 259 " pdb=" CA ARG l 259 " pdb=" CB ARG l 259 " ideal model delta sigma weight residual 110.29 117.84 -7.55 1.52e+00 4.33e-01 2.47e+01 angle pdb=" N ARG N 259 " pdb=" CA ARG N 259 " pdb=" CB ARG N 259 " ideal model delta sigma weight residual 110.29 117.82 -7.53 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N ARG T 259 " pdb=" CA ARG T 259 " pdb=" CB ARG T 259 " ideal model delta sigma weight residual 110.29 117.82 -7.53 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N ARG o 259 " pdb=" CA ARG o 259 " pdb=" CB ARG o 259 " ideal model delta sigma weight residual 110.29 117.81 -7.52 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N ARG i 259 " pdb=" CA ARG i 259 " pdb=" CB ARG i 259 " ideal model delta sigma weight residual 110.29 117.81 -7.52 1.52e+00 4.33e-01 2.45e+01 ... (remaining 53125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 21404 16.67 - 33.34: 1662 33.34 - 50.01: 328 50.01 - 66.68: 56 66.68 - 83.35: 14 Dihedral angle restraints: 23464 sinusoidal: 9310 harmonic: 14154 Sorted by residual: dihedral pdb=" CA ARG K 259 " pdb=" C ARG K 259 " pdb=" N ARG K 260 " pdb=" CA ARG K 260 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG o 259 " pdb=" C ARG o 259 " pdb=" N ARG o 260 " pdb=" CA ARG o 260 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG i 259 " pdb=" C ARG i 259 " pdb=" N ARG i 260 " pdb=" CA ARG i 260 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 23461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3135 0.031 - 0.062: 1535 0.062 - 0.092: 712 0.092 - 0.123: 297 0.123 - 0.154: 117 Chirality restraints: 5796 Sorted by residual: chirality pdb=" CA VAL l 258 " pdb=" N VAL l 258 " pdb=" C VAL l 258 " pdb=" CB VAL l 258 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL Q 258 " pdb=" N VAL Q 258 " pdb=" C VAL Q 258 " pdb=" CB VAL Q 258 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA VAL N 258 " pdb=" N VAL N 258 " pdb=" C VAL N 258 " pdb=" CB VAL N 258 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 5793 not shown) Planarity restraints: 7084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN N 223 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO N 224 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO N 224 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 224 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 223 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO B 224 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 224 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 224 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Q 223 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO Q 224 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 224 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 224 " 0.025 5.00e-02 4.00e+02 ... (remaining 7081 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6155 2.76 - 3.29: 34002 3.29 - 3.83: 64616 3.83 - 4.36: 79971 4.36 - 4.90: 141953 Nonbonded interactions: 326697 Sorted by model distance: nonbonded pdb=" OD1 ASP W 165 " pdb=" NH2 ARG W 233 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG B 233 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP H 165 " pdb=" NH2 ARG H 233 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP T 165 " pdb=" NH2 ARG T 233 " model vdw 2.224 3.120 nonbonded pdb=" OD1 ASP N 165 " pdb=" NH2 ARG N 233 " model vdw 2.225 3.120 ... (remaining 326692 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.800 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.008 0.044 39214 Z= 0.340 Angle : 0.674 7.553 53158 Z= 0.387 Chirality : 0.049 0.154 5796 Planarity : 0.004 0.045 7084 Dihedral : 12.450 83.348 14406 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.11), residues: 4942 helix: 2.26 (0.19), residues: 784 sheet: 0.85 (0.15), residues: 1022 loop : -0.24 (0.10), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG o 259 TYR 0.017 0.002 TYR o 194 PHE 0.019 0.002 PHE Z 195 TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS J 305 Details of bonding type rmsd covalent geometry : bond 0.00805 (39200) covalent geometry : angle 0.67398 (53130) SS BOND : bond 0.00223 ( 14) SS BOND : angle 0.11931 ( 28) hydrogen bonds : bond 0.18515 ( 1555) hydrogen bonds : angle 7.40631 ( 3993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 1.567 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: E 145 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8710 (mp0) REVERT: G 209 GLN cc_start: 0.8898 (mt0) cc_final: 0.8696 (mt0) REVERT: Q 145 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8579 (mp0) REVERT: l 145 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8571 (mp0) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 1.1264 time to fit residues: 1040.1340 Evaluate side-chains 585 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN G 374 ASN H 201 ASN J 188 GLN K 201 ASN M 188 GLN M 360 ASN P 374 ASN Q 201 ASN S 360 ASN T 201 ASN Y 188 GLN c 201 ASN e 188 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 201 ASN h 188 GLN h 263 GLN h 360 ASN k 374 ASN l 201 ASN n 360 ASN o 201 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.036663 restraints weight = 115616.580| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 3.13 r_work: 0.2382 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 39214 Z= 0.279 Angle : 0.647 6.817 53158 Z= 0.338 Chirality : 0.044 0.139 5796 Planarity : 0.005 0.055 7084 Dihedral : 4.561 14.862 5502 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.56 % Allowed : 10.58 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.12), residues: 4942 helix: 2.25 (0.19), residues: 798 sheet: 0.64 (0.17), residues: 938 loop : 0.07 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 151 TYR 0.009 0.001 TYR V 387 PHE 0.029 0.002 PHE K 195 TRP 0.012 0.001 TRP b 307 HIS 0.002 0.001 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00633 (39200) covalent geometry : angle 0.64732 (53130) SS BOND : bond 0.00088 ( 14) SS BOND : angle 0.25353 ( 28) hydrogen bonds : bond 0.04375 ( 1555) hydrogen bonds : angle 5.81077 ( 3993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 652 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 353 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8915 (mm-30) REVERT: A 357 ASN cc_start: 0.9134 (m-40) cc_final: 0.8688 (m110) REVERT: A 390 GLU cc_start: 0.7953 (pp20) cc_final: 0.7480 (pp20) REVERT: B 159 LYS cc_start: 0.8893 (mppt) cc_final: 0.8642 (mppt) REVERT: B 161 MET cc_start: 0.9410 (mmm) cc_final: 0.9077 (mmm) REVERT: B 263 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8840 (ttpp) REVERT: D 276 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8478 (tm-30) REVERT: D 371 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: D 390 GLU cc_start: 0.7952 (pp20) cc_final: 0.7543 (pp20) REVERT: E 141 ARG cc_start: 0.8987 (ttp80) cc_final: 0.8655 (tmm-80) REVERT: E 145 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8940 (mp0) REVERT: E 159 LYS cc_start: 0.8940 (mppt) cc_final: 0.8682 (mppt) REVERT: E 161 MET cc_start: 0.9427 (mmm) cc_final: 0.8584 (mmm) REVERT: E 240 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8731 (mm-30) REVERT: E 259 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8858 (ttm110) REVERT: G 276 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8498 (tm-30) REVERT: G 284 ASN cc_start: 0.9152 (m110) cc_final: 0.8940 (m-40) REVERT: G 353 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8716 (mm-30) REVERT: G 357 ASN cc_start: 0.9157 (m-40) cc_final: 0.8707 (m110) REVERT: G 371 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8538 (mt-10) REVERT: G 390 GLU cc_start: 0.8888 (pt0) cc_final: 0.8498 (pp20) REVERT: H 141 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8668 (tmm-80) REVERT: H 145 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (mp0) REVERT: H 159 LYS cc_start: 0.8959 (mppt) cc_final: 0.8742 (mppt) REVERT: H 161 MET cc_start: 0.9515 (mmm) cc_final: 0.9294 (mmm) REVERT: H 162 MET cc_start: 0.9562 (ptt) cc_final: 0.8377 (ptp) REVERT: H 263 LYS cc_start: 0.9288 (ttpp) cc_final: 0.8629 (ttpp) REVERT: I 32 GLU cc_start: 0.9311 (pt0) cc_final: 0.8561 (pm20) REVERT: J 185 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: J 276 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8465 (tm-30) REVERT: J 353 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8785 (mm-30) REVERT: J 357 ASN cc_start: 0.9153 (m-40) cc_final: 0.8733 (m110) REVERT: J 390 GLU cc_start: 0.7921 (pp20) cc_final: 0.7581 (pp20) REVERT: K 141 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8699 (tmm-80) REVERT: K 145 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8883 (mp0) REVERT: K 159 LYS cc_start: 0.8935 (mppt) cc_final: 0.8629 (mppt) REVERT: K 161 MET cc_start: 0.9475 (mmm) cc_final: 0.8915 (mmm) REVERT: K 240 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8795 (mm-30) REVERT: K 263 LYS cc_start: 0.9232 (ptmm) cc_final: 0.8802 (ttpp) REVERT: L 32 GLU cc_start: 0.9321 (pt0) cc_final: 0.9112 (pt0) REVERT: M 276 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8482 (tm-30) REVERT: M 353 GLU cc_start: 0.9287 (tp30) cc_final: 0.8969 (tp30) REVERT: M 357 ASN cc_start: 0.9166 (m-40) cc_final: 0.8838 (m110) REVERT: M 371 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8607 (mt-10) REVERT: M 390 GLU cc_start: 0.7848 (pp20) cc_final: 0.7482 (pp20) REVERT: N 141 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8689 (tmm-80) REVERT: N 145 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8811 (mp0) REVERT: N 159 LYS cc_start: 0.8955 (mppt) cc_final: 0.8744 (mppt) REVERT: N 161 MET cc_start: 0.9497 (mmm) cc_final: 0.9090 (mmm) REVERT: N 240 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8837 (mm-30) REVERT: N 259 ARG cc_start: 0.9096 (ttm-80) cc_final: 0.8887 (ttm110) REVERT: P 185 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: P 276 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8485 (tm-30) REVERT: P 319 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9204 (mp) REVERT: P 371 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8544 (mt-10) REVERT: P 390 GLU cc_start: 0.7880 (pp20) cc_final: 0.7610 (pp20) REVERT: Q 145 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8971 (mp0) REVERT: Q 159 LYS cc_start: 0.8945 (mppt) cc_final: 0.8698 (mppt) REVERT: Q 161 MET cc_start: 0.9477 (mmm) cc_final: 0.9110 (mmm) REVERT: Q 240 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8821 (mm-30) REVERT: S 276 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8435 (tm-30) REVERT: S 353 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8910 (mm-30) REVERT: S 357 ASN cc_start: 0.9226 (m-40) cc_final: 0.8852 (m110) REVERT: S 390 GLU cc_start: 0.7776 (pp20) cc_final: 0.7440 (pp20) REVERT: T 145 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8841 (mp0) REVERT: T 159 LYS cc_start: 0.8859 (mppt) cc_final: 0.8515 (mppt) REVERT: T 225 LYS cc_start: 0.9369 (ttmt) cc_final: 0.9089 (ttmt) REVERT: T 240 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8719 (mm-30) REVERT: T 263 LYS cc_start: 0.9214 (ttpp) cc_final: 0.8850 (ttpp) REVERT: V 276 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8353 (tm-30) REVERT: V 353 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8912 (mm-30) REVERT: V 357 ASN cc_start: 0.9163 (m-40) cc_final: 0.8775 (m110) REVERT: V 390 GLU cc_start: 0.7913 (pp20) cc_final: 0.7407 (pp20) REVERT: W 159 LYS cc_start: 0.8903 (mppt) cc_final: 0.8644 (mppt) REVERT: W 161 MET cc_start: 0.9398 (mmm) cc_final: 0.9093 (mmm) REVERT: W 240 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8822 (mm-30) REVERT: W 263 LYS cc_start: 0.9201 (ttpp) cc_final: 0.8802 (ttpp) REVERT: Y 276 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8476 (tm-30) REVERT: Y 371 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: Y 390 GLU cc_start: 0.7976 (pp20) cc_final: 0.7482 (pp20) REVERT: Z 141 ARG cc_start: 0.8919 (ttp80) cc_final: 0.8642 (tmm-80) REVERT: Z 159 LYS cc_start: 0.8959 (mppt) cc_final: 0.8717 (mppt) REVERT: Z 161 MET cc_start: 0.9421 (mmm) cc_final: 0.8882 (mmm) REVERT: Z 240 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8735 (mm-30) REVERT: Z 259 ARG cc_start: 0.9071 (ttm-80) cc_final: 0.8868 (ttm110) REVERT: b 276 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8434 (tm-30) REVERT: b 284 ASN cc_start: 0.9133 (m110) cc_final: 0.8922 (m-40) REVERT: b 353 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8687 (mm-30) REVERT: b 357 ASN cc_start: 0.9163 (m-40) cc_final: 0.8677 (m110) REVERT: b 371 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8525 (mt-10) REVERT: b 390 GLU cc_start: 0.8093 (pp20) cc_final: 0.7733 (pp20) REVERT: c 141 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8633 (ttp80) REVERT: c 145 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: c 159 LYS cc_start: 0.8950 (mppt) cc_final: 0.8726 (mppt) REVERT: c 161 MET cc_start: 0.9407 (mmm) cc_final: 0.8259 (mmm) REVERT: c 162 MET cc_start: 0.9577 (ptt) cc_final: 0.8479 (ptp) REVERT: c 259 ARG cc_start: 0.9074 (tpp80) cc_final: 0.8809 (ttm-80) REVERT: c 263 LYS cc_start: 0.9318 (ttpp) cc_final: 0.8659 (ttpp) REVERT: d 32 GLU cc_start: 0.9364 (pt0) cc_final: 0.8885 (pm20) REVERT: e 185 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (mp0) REVERT: e 276 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8452 (tm-30) REVERT: e 353 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8782 (mm-30) REVERT: e 357 ASN cc_start: 0.9151 (m-40) cc_final: 0.8723 (m110) REVERT: e 390 GLU cc_start: 0.7859 (pp20) cc_final: 0.7507 (pp20) REVERT: f 145 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8791 (mp0) REVERT: f 159 LYS cc_start: 0.8895 (mppt) cc_final: 0.8680 (mppt) REVERT: f 161 MET cc_start: 0.9412 (mmm) cc_final: 0.8834 (mmm) REVERT: f 240 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8759 (mm-30) REVERT: h 276 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8484 (tm-30) REVERT: h 353 GLU cc_start: 0.9364 (tp30) cc_final: 0.9038 (tp30) REVERT: h 357 ASN cc_start: 0.9179 (m-40) cc_final: 0.8835 (m110) REVERT: h 371 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8594 (mt-10) REVERT: h 390 GLU cc_start: 0.7825 (pp20) cc_final: 0.7560 (pp20) REVERT: i 141 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8487 (ttp80) REVERT: i 145 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: i 159 LYS cc_start: 0.8952 (mppt) cc_final: 0.8708 (mppt) REVERT: i 161 MET cc_start: 0.9501 (mmm) cc_final: 0.9135 (mmm) REVERT: i 240 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8809 (mm-30) REVERT: i 259 ARG cc_start: 0.9094 (ttm-80) cc_final: 0.8876 (ttm110) REVERT: i 263 LYS cc_start: 0.9227 (ttpp) cc_final: 0.8876 (ttpp) REVERT: k 276 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8483 (tm-30) REVERT: k 319 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9201 (mp) REVERT: k 390 GLU cc_start: 0.8078 (pp20) cc_final: 0.7587 (pp20) REVERT: l 145 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8966 (mp0) REVERT: l 159 LYS cc_start: 0.8950 (mppt) cc_final: 0.8712 (mppt) REVERT: l 161 MET cc_start: 0.9471 (mmm) cc_final: 0.9104 (mmm) REVERT: l 240 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8819 (mm-30) REVERT: n 276 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8433 (tm-30) REVERT: n 353 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8906 (mm-30) REVERT: n 357 ASN cc_start: 0.9216 (m-40) cc_final: 0.8828 (m110) REVERT: n 390 GLU cc_start: 0.7844 (pp20) cc_final: 0.7596 (pp20) REVERT: o 145 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (mp0) REVERT: o 159 LYS cc_start: 0.8894 (mppt) cc_final: 0.8566 (mppt) REVERT: o 240 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8716 (mm-30) REVERT: o 263 LYS cc_start: 0.9211 (ttpp) cc_final: 0.8848 (ttpp) outliers start: 63 outliers final: 12 residues processed: 675 average time/residue: 1.1569 time to fit residues: 887.3806 Evaluate side-chains 614 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 587 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain M residue 209 GLN Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain V residue 319 ILE Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain h residue 209 GLN Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain n residue 319 ILE Chi-restraints excluded: chain o residue 145 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 482 optimal weight: 10.0000 chunk 480 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 355 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 335 optimal weight: 3.9990 chunk 448 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN D 357 ASN D 360 ASN D 374 ASN G 374 ASN J 374 ASN M 263 GLN M 360 ASN M 374 ASN P 357 ASN P 374 ASN S 284 ASN S 374 ASN V 374 ASN Y 357 ASN Y 360 ASN Y 374 ASN b 374 ASN e 374 ASN h 360 ASN h 374 ASN k 357 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 284 ASN n 374 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.036551 restraints weight = 117088.454| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 3.18 r_work: 0.2372 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 39214 Z= 0.225 Angle : 0.583 8.331 53158 Z= 0.306 Chirality : 0.043 0.134 5796 Planarity : 0.004 0.044 7084 Dihedral : 4.327 14.761 5502 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.78 % Allowed : 14.63 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.12), residues: 4942 helix: 2.19 (0.19), residues: 798 sheet: 0.56 (0.17), residues: 938 loop : 0.17 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 141 TYR 0.007 0.001 TYR b 387 PHE 0.026 0.001 PHE Q 195 TRP 0.008 0.001 TRP D 307 HIS 0.002 0.000 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00517 (39200) covalent geometry : angle 0.58285 (53130) SS BOND : bond 0.00097 ( 14) SS BOND : angle 0.32158 ( 28) hydrogen bonds : bond 0.03791 ( 1555) hydrogen bonds : angle 5.56476 ( 3993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 613 time to evaluate : 1.609 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: A 276 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 308 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: A 353 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8903 (mm-30) REVERT: A 357 ASN cc_start: 0.9118 (m-40) cc_final: 0.8719 (m110) REVERT: A 374 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8808 (t0) REVERT: A 390 GLU cc_start: 0.8009 (pp20) cc_final: 0.7539 (pp20) REVERT: B 159 LYS cc_start: 0.8928 (mppt) cc_final: 0.8636 (mppt) REVERT: B 161 MET cc_start: 0.9365 (mmm) cc_final: 0.8898 (mmm) REVERT: B 263 LYS cc_start: 0.9249 (ttpp) cc_final: 0.8923 (ttpp) REVERT: D 276 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8522 (tm-30) REVERT: D 308 GLU cc_start: 0.8624 (mp0) cc_final: 0.8318 (mp0) REVERT: D 353 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8967 (mm-30) REVERT: D 371 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: D 390 GLU cc_start: 0.7987 (pp20) cc_final: 0.7466 (pp20) REVERT: E 145 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8975 (mp0) REVERT: E 159 LYS cc_start: 0.9008 (mppt) cc_final: 0.8686 (mppt) REVERT: E 161 MET cc_start: 0.9402 (mmm) cc_final: 0.8826 (mmm) REVERT: E 240 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8872 (mm-30) REVERT: E 259 ARG cc_start: 0.8992 (ttm-80) cc_final: 0.8780 (ttm110) REVERT: F 32 GLU cc_start: 0.9257 (pt0) cc_final: 0.8914 (pm20) REVERT: G 276 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8512 (tm-30) REVERT: G 284 ASN cc_start: 0.9128 (m110) cc_final: 0.8913 (m-40) REVERT: G 308 GLU cc_start: 0.8542 (mp0) cc_final: 0.8188 (mp0) REVERT: G 353 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8689 (mm-30) REVERT: G 357 ASN cc_start: 0.9149 (m-40) cc_final: 0.8671 (m110) REVERT: G 371 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8631 (mt-10) REVERT: G 390 GLU cc_start: 0.8796 (pt0) cc_final: 0.8525 (pp20) REVERT: H 145 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8880 (mp0) REVERT: H 159 LYS cc_start: 0.8995 (mppt) cc_final: 0.8732 (mppt) REVERT: H 161 MET cc_start: 0.9437 (mmm) cc_final: 0.9164 (mmm) REVERT: H 263 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9048 (ttpp) REVERT: J 185 GLU cc_start: 0.8898 (mp0) cc_final: 0.8658 (mp0) REVERT: J 276 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8506 (tm-30) REVERT: J 353 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8760 (mm-30) REVERT: J 357 ASN cc_start: 0.9160 (m-40) cc_final: 0.8724 (m110) REVERT: J 390 GLU cc_start: 0.7968 (pp20) cc_final: 0.7539 (pp20) REVERT: K 145 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: K 159 LYS cc_start: 0.8984 (mppt) cc_final: 0.8630 (mppt) REVERT: K 161 MET cc_start: 0.9469 (mmm) cc_final: 0.8948 (mmm) REVERT: K 240 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8899 (mm-30) REVERT: K 263 LYS cc_start: 0.9233 (ptmm) cc_final: 0.8954 (ttpp) REVERT: M 276 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8510 (tm-30) REVERT: M 353 GLU cc_start: 0.9342 (tp30) cc_final: 0.9009 (tp30) REVERT: M 357 ASN cc_start: 0.9115 (m-40) cc_final: 0.8786 (m110) REVERT: M 371 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8690 (mt-10) REVERT: M 390 GLU cc_start: 0.7842 (pp20) cc_final: 0.7379 (pp20) REVERT: N 141 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8755 (tmm-80) REVERT: N 159 LYS cc_start: 0.8926 (mppt) cc_final: 0.8620 (mppt) REVERT: N 161 MET cc_start: 0.9442 (mmm) cc_final: 0.8992 (mmm) REVERT: P 185 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: P 276 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8558 (tm-30) REVERT: P 319 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9226 (mp) REVERT: P 374 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8732 (t0) REVERT: P 390 GLU cc_start: 0.7831 (pp20) cc_final: 0.7627 (pp20) REVERT: Q 141 ARG cc_start: 0.9071 (ttp80) cc_final: 0.8644 (tmm-80) REVERT: Q 145 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8931 (OUTLIER) REVERT: Q 159 LYS cc_start: 0.8977 (mppt) cc_final: 0.8721 (mppt) REVERT: Q 161 MET cc_start: 0.9448 (mmm) cc_final: 0.9043 (mmm) REVERT: S 276 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8510 (tm-30) REVERT: S 308 GLU cc_start: 0.8531 (mp0) cc_final: 0.8303 (mp0) REVERT: S 353 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8682 (tp30) REVERT: S 357 ASN cc_start: 0.9220 (m-40) cc_final: 0.8676 (m110) REVERT: S 390 GLU cc_start: 0.7874 (pp20) cc_final: 0.7413 (pp20) REVERT: T 141 ARG cc_start: 0.8794 (tmm-80) cc_final: 0.8497 (ttp80) REVERT: T 145 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8717 (mp0) REVERT: T 159 LYS cc_start: 0.8931 (mppt) cc_final: 0.8531 (mppt) REVERT: T 240 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8714 (mm-30) REVERT: T 263 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8853 (ttpp) REVERT: V 276 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8486 (tm-30) REVERT: V 308 GLU cc_start: 0.8580 (mp0) cc_final: 0.8288 (mp0) REVERT: V 353 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8906 (mm-30) REVERT: V 357 ASN cc_start: 0.9139 (m-40) cc_final: 0.8743 (m110) REVERT: V 390 GLU cc_start: 0.7991 (pp20) cc_final: 0.7509 (pp20) REVERT: W 141 ARG cc_start: 0.9022 (ttp80) cc_final: 0.8714 (ttp80) REVERT: W 159 LYS cc_start: 0.8950 (mppt) cc_final: 0.8650 (mppt) REVERT: W 161 MET cc_start: 0.9390 (mmm) cc_final: 0.8908 (mmm) REVERT: W 263 LYS cc_start: 0.9258 (ttpp) cc_final: 0.8904 (ttpp) REVERT: Y 276 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8530 (tm-30) REVERT: Y 308 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: Y 353 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8932 (mm-30) REVERT: Y 371 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: Y 390 GLU cc_start: 0.8079 (pp20) cc_final: 0.7415 (pp20) REVERT: Z 159 LYS cc_start: 0.9014 (mppt) cc_final: 0.8707 (mppt) REVERT: Z 161 MET cc_start: 0.9392 (mmm) cc_final: 0.8835 (mmm) REVERT: Z 240 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8877 (mm-30) REVERT: Z 259 ARG cc_start: 0.9000 (ttm-80) cc_final: 0.8789 (ttm110) REVERT: b 276 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8504 (tm-30) REVERT: b 284 ASN cc_start: 0.9122 (m110) cc_final: 0.8906 (m-40) REVERT: b 308 GLU cc_start: 0.8589 (mp0) cc_final: 0.8232 (mp0) REVERT: b 353 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8692 (mm-30) REVERT: b 357 ASN cc_start: 0.9163 (m-40) cc_final: 0.8675 (m110) REVERT: b 371 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8604 (mt-10) REVERT: b 390 GLU cc_start: 0.8022 (pp20) cc_final: 0.7715 (pp20) REVERT: c 141 ARG cc_start: 0.8879 (ttp80) cc_final: 0.8516 (ttp80) REVERT: c 145 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: c 159 LYS cc_start: 0.9000 (mppt) cc_final: 0.8786 (mppt) REVERT: c 161 MET cc_start: 0.9386 (mmm) cc_final: 0.9027 (mpp) REVERT: c 162 MET cc_start: 0.9627 (ptt) cc_final: 0.8526 (ptp) REVERT: c 259 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8687 (ttm-80) REVERT: c 263 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9065 (ttpp) REVERT: d 32 GLU cc_start: 0.9400 (pt0) cc_final: 0.8657 (pm20) REVERT: e 185 GLU cc_start: 0.8916 (mp0) cc_final: 0.8678 (mp0) REVERT: e 276 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8518 (tm-30) REVERT: e 353 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8783 (mm-30) REVERT: e 357 ASN cc_start: 0.9165 (m-40) cc_final: 0.8705 (m110) REVERT: e 390 GLU cc_start: 0.7943 (pp20) cc_final: 0.7501 (pp20) REVERT: f 141 ARG cc_start: 0.8850 (tmm-80) cc_final: 0.8423 (ttp80) REVERT: f 145 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: f 159 LYS cc_start: 0.8927 (mppt) cc_final: 0.8655 (mppt) REVERT: f 161 MET cc_start: 0.9417 (mmm) cc_final: 0.8820 (mmm) REVERT: f 240 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8859 (mm-30) REVERT: h 276 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8509 (tm-30) REVERT: h 353 GLU cc_start: 0.9387 (tp30) cc_final: 0.9020 (tp30) REVERT: h 357 ASN cc_start: 0.9144 (m-40) cc_final: 0.8806 (m110) REVERT: h 371 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8665 (mt-10) REVERT: h 390 GLU cc_start: 0.7876 (pp20) cc_final: 0.7388 (pp20) REVERT: i 159 LYS cc_start: 0.8926 (mppt) cc_final: 0.8624 (mppt) REVERT: i 161 MET cc_start: 0.9440 (mmm) cc_final: 0.8964 (mmm) REVERT: i 263 LYS cc_start: 0.9241 (ttpp) cc_final: 0.8876 (ttpp) REVERT: k 276 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8567 (tm-30) REVERT: k 371 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8671 (mt-10) REVERT: k 374 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8756 (t0) REVERT: k 390 GLU cc_start: 0.8051 (pp20) cc_final: 0.7633 (pp20) REVERT: l 141 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8596 (tmm-80) REVERT: l 145 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8948 (OUTLIER) REVERT: l 159 LYS cc_start: 0.8978 (mppt) cc_final: 0.8699 (mppt) REVERT: l 161 MET cc_start: 0.9454 (mmm) cc_final: 0.9050 (mmm) REVERT: n 276 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8515 (tm-30) REVERT: n 308 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: n 353 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8694 (tp30) REVERT: n 357 ASN cc_start: 0.9195 (m-40) cc_final: 0.8677 (m110) REVERT: n 390 GLU cc_start: 0.7857 (pp20) cc_final: 0.7461 (pp20) REVERT: o 141 ARG cc_start: 0.8797 (tmm-80) cc_final: 0.8510 (ttp80) REVERT: o 145 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: o 159 LYS cc_start: 0.8936 (mppt) cc_final: 0.8534 (mppt) REVERT: o 240 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8715 (mm-30) REVERT: o 263 LYS cc_start: 0.9259 (ttpp) cc_final: 0.8860 (ttpp) outliers start: 72 outliers final: 15 residues processed: 646 average time/residue: 1.1782 time to fit residues: 863.5264 Evaluate side-chains 606 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 575 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 209 GLN Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain P residue 374 ASN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 155 TYR Chi-restraints excluded: chain c residue 263 LYS Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain h residue 209 GLN Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain k residue 374 ASN Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 31 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 243 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 488 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 360 ASN D 374 ASN G 374 ASN J 188 GLN J 374 ASN M 188 GLN M 360 ASN M 374 ASN N 201 ASN P 357 ASN S 374 ASN ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 360 ASN Y 374 ASN b 374 ASN e 188 GLN e 374 ASN h 188 GLN h 360 ASN h 374 ASN i 201 ASN k 357 ASN k 374 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.037793 restraints weight = 114903.300| |-----------------------------------------------------------------------------| r_work (start): 0.2556 rms_B_bonded: 3.17 r_work: 0.2410 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39214 Z= 0.119 Angle : 0.551 9.008 53158 Z= 0.287 Chirality : 0.043 0.140 5796 Planarity : 0.004 0.044 7084 Dihedral : 4.083 15.793 5502 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.51 % Allowed : 16.44 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.12), residues: 4942 helix: 2.09 (0.19), residues: 798 sheet: 0.55 (0.17), residues: 938 loop : 0.19 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 141 TYR 0.009 0.001 TYR T 155 PHE 0.026 0.001 PHE W 195 TRP 0.007 0.001 TRP D 307 HIS 0.001 0.000 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00280 (39200) covalent geometry : angle 0.55130 (53130) SS BOND : bond 0.00203 ( 14) SS BOND : angle 0.32257 ( 28) hydrogen bonds : bond 0.03177 ( 1555) hydrogen bonds : angle 5.41891 ( 3993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 656 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8463 (tm-30) REVERT: A 308 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: A 353 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8766 (mm-30) REVERT: A 357 ASN cc_start: 0.9062 (m-40) cc_final: 0.8652 (m110) REVERT: A 371 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8568 (mt-10) REVERT: A 390 GLU cc_start: 0.8013 (pp20) cc_final: 0.7641 (pp20) REVERT: B 159 LYS cc_start: 0.8935 (mppt) cc_final: 0.8643 (mppt) REVERT: B 161 MET cc_start: 0.9401 (mmm) cc_final: 0.9108 (mmm) REVERT: B 263 LYS cc_start: 0.9304 (ttpp) cc_final: 0.8958 (ttpp) REVERT: D 276 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8512 (tm-30) REVERT: D 371 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8334 (mt-10) REVERT: D 390 GLU cc_start: 0.8019 (pp20) cc_final: 0.7443 (pp20) REVERT: E 145 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8986 (mp0) REVERT: E 159 LYS cc_start: 0.9037 (mppt) cc_final: 0.8745 (mppt) REVERT: E 161 MET cc_start: 0.9394 (mmm) cc_final: 0.8809 (mmm) REVERT: E 240 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8958 (mm-30) REVERT: F 30 ASN cc_start: 0.8197 (p0) cc_final: 0.7679 (p0) REVERT: G 276 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8520 (tm-30) REVERT: G 308 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: G 353 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8593 (mm-30) REVERT: G 357 ASN cc_start: 0.9137 (m-40) cc_final: 0.8595 (m110) REVERT: G 371 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8623 (mt-10) REVERT: G 390 GLU cc_start: 0.8768 (pt0) cc_final: 0.8259 (pp20) REVERT: H 141 ARG cc_start: 0.8902 (ttp80) cc_final: 0.8532 (ttp80) REVERT: H 145 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: H 159 LYS cc_start: 0.9004 (mppt) cc_final: 0.8743 (mppt) REVERT: H 161 MET cc_start: 0.9431 (mmm) cc_final: 0.9134 (mmm) REVERT: H 263 LYS cc_start: 0.9283 (ttpp) cc_final: 0.9003 (ttpp) REVERT: J 185 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8666 (mp0) REVERT: J 276 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8536 (tm-30) REVERT: J 308 GLU cc_start: 0.8490 (mp0) cc_final: 0.8193 (mp0) REVERT: J 353 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8721 (mm-30) REVERT: J 357 ASN cc_start: 0.9147 (m-40) cc_final: 0.8702 (m110) REVERT: J 390 GLU cc_start: 0.7988 (pp20) cc_final: 0.7644 (pp20) REVERT: K 141 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8542 (ttp80) REVERT: K 145 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: K 159 LYS cc_start: 0.9012 (mppt) cc_final: 0.8674 (mppt) REVERT: K 161 MET cc_start: 0.9470 (mmm) cc_final: 0.8940 (mmm) REVERT: K 240 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8979 (mm-30) REVERT: L 32 GLU cc_start: 0.9253 (pt0) cc_final: 0.8979 (pt0) REVERT: M 276 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8467 (tm-30) REVERT: M 353 GLU cc_start: 0.9339 (tp30) cc_final: 0.8960 (tp30) REVERT: M 357 ASN cc_start: 0.9069 (m-40) cc_final: 0.8780 (m110) REVERT: M 371 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8680 (mt-10) REVERT: M 390 GLU cc_start: 0.7909 (pp20) cc_final: 0.7568 (pp20) REVERT: N 141 ARG cc_start: 0.8965 (ttp80) cc_final: 0.8636 (ttp80) REVERT: N 145 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8679 (mp0) REVERT: N 159 LYS cc_start: 0.8926 (mppt) cc_final: 0.8611 (mppt) REVERT: N 161 MET cc_start: 0.9429 (mmm) cc_final: 0.9080 (mmm) REVERT: P 185 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: P 276 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8546 (tm-30) REVERT: P 308 GLU cc_start: 0.8596 (mp0) cc_final: 0.8222 (mp0) REVERT: P 371 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8432 (mt-10) REVERT: P 390 GLU cc_start: 0.7825 (pp20) cc_final: 0.7506 (pp20) REVERT: Q 141 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8693 (tmm-80) REVERT: Q 145 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8930 (OUTLIER) REVERT: Q 159 LYS cc_start: 0.8974 (mppt) cc_final: 0.8681 (mppt) REVERT: Q 161 MET cc_start: 0.9386 (mmm) cc_final: 0.9122 (mmm) REVERT: Q 183 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8832 (ttmm) REVERT: R 30 ASN cc_start: 0.8110 (p0) cc_final: 0.7882 (p0) REVERT: S 276 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8476 (tm-30) REVERT: S 308 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: S 353 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8630 (tp30) REVERT: S 357 ASN cc_start: 0.9195 (m-40) cc_final: 0.8633 (m110) REVERT: S 374 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8831 (t0) REVERT: S 390 GLU cc_start: 0.7943 (pp20) cc_final: 0.7659 (pp20) REVERT: T 141 ARG cc_start: 0.8815 (tmm-80) cc_final: 0.8442 (ttp80) REVERT: T 145 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: T 159 LYS cc_start: 0.8975 (mppt) cc_final: 0.8543 (mppt) REVERT: T 240 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8754 (mm-30) REVERT: T 263 LYS cc_start: 0.9273 (ttpp) cc_final: 0.8961 (ttpp) REVERT: V 276 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8433 (tm-30) REVERT: V 353 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8773 (mm-30) REVERT: V 357 ASN cc_start: 0.9094 (m-40) cc_final: 0.8671 (m110) REVERT: V 390 GLU cc_start: 0.8026 (pp20) cc_final: 0.7581 (pp20) REVERT: W 159 LYS cc_start: 0.8954 (mppt) cc_final: 0.8614 (mppt) REVERT: W 161 MET cc_start: 0.9427 (mmm) cc_final: 0.9069 (mmm) REVERT: W 263 LYS cc_start: 0.9291 (ttpp) cc_final: 0.8924 (ttpp) REVERT: Y 276 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8502 (tm-30) REVERT: Y 308 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: Y 371 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8344 (mt-10) REVERT: Y 390 GLU cc_start: 0.8109 (pp20) cc_final: 0.7704 (pp20) REVERT: Z 141 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8524 (ttp80) REVERT: Z 145 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: Z 159 LYS cc_start: 0.9035 (mppt) cc_final: 0.8718 (mppt) REVERT: Z 161 MET cc_start: 0.9391 (mmm) cc_final: 0.8802 (mmm) REVERT: Z 240 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8977 (mm-30) REVERT: b 276 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8517 (tm-30) REVERT: b 308 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: b 353 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8598 (mm-30) REVERT: b 357 ASN cc_start: 0.9154 (m-40) cc_final: 0.8599 (m110) REVERT: c 145 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8731 (mp0) REVERT: c 159 LYS cc_start: 0.8996 (mppt) cc_final: 0.8754 (mppt) REVERT: c 161 MET cc_start: 0.9393 (mmm) cc_final: 0.8269 (mmm) REVERT: c 162 MET cc_start: 0.9637 (ptt) cc_final: 0.8469 (ptp) REVERT: c 263 LYS cc_start: 0.9304 (ttpp) cc_final: 0.9028 (ttpp) REVERT: d 32 GLU cc_start: 0.9412 (pt0) cc_final: 0.8852 (pm20) REVERT: e 185 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8674 (mp0) REVERT: e 276 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8528 (tm-30) REVERT: e 353 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8640 (mm-30) REVERT: e 357 ASN cc_start: 0.9158 (m-40) cc_final: 0.8701 (m110) REVERT: e 390 GLU cc_start: 0.7933 (pp20) cc_final: 0.7585 (pp20) REVERT: f 145 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8787 (mp0) REVERT: f 159 LYS cc_start: 0.8895 (mppt) cc_final: 0.8627 (mppt) REVERT: f 161 MET cc_start: 0.9397 (mmm) cc_final: 0.8788 (mmm) REVERT: f 202 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9047 (mt-10) REVERT: f 227 MET cc_start: 0.9408 (tpt) cc_final: 0.8698 (tpt) REVERT: f 240 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8931 (mm-30) REVERT: h 276 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8434 (tm-30) REVERT: h 353 GLU cc_start: 0.9372 (tp30) cc_final: 0.8978 (tp30) REVERT: h 357 ASN cc_start: 0.9108 (m-40) cc_final: 0.8779 (m110) REVERT: h 371 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8675 (mt-10) REVERT: i 141 ARG cc_start: 0.8828 (tmm-80) cc_final: 0.8515 (ttp80) REVERT: i 145 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: i 159 LYS cc_start: 0.8927 (mppt) cc_final: 0.8616 (mppt) REVERT: i 161 MET cc_start: 0.9431 (mmm) cc_final: 0.9101 (mmm) REVERT: k 276 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8545 (tm-30) REVERT: k 371 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8498 (mt-10) REVERT: k 374 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8734 (t0) REVERT: k 390 GLU cc_start: 0.7992 (pp20) cc_final: 0.7436 (pp20) REVERT: l 141 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8712 (tmm-80) REVERT: l 145 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8948 (mp0) REVERT: l 159 LYS cc_start: 0.8974 (mppt) cc_final: 0.8686 (mppt) REVERT: l 161 MET cc_start: 0.9374 (mmm) cc_final: 0.9109 (mmm) REVERT: m 30 ASN cc_start: 0.8037 (p0) cc_final: 0.7817 (p0) REVERT: n 276 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8487 (tm-30) REVERT: n 308 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: n 353 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8634 (tp30) REVERT: n 357 ASN cc_start: 0.9187 (m-40) cc_final: 0.8642 (m110) REVERT: n 374 ASN cc_start: 0.9112 (m-40) cc_final: 0.8847 (t0) REVERT: n 390 GLU cc_start: 0.7878 (pp20) cc_final: 0.7540 (pp20) REVERT: o 159 LYS cc_start: 0.8977 (mppt) cc_final: 0.8548 (mppt) REVERT: o 240 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8747 (mm-30) REVERT: o 259 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8640 (ttm-80) REVERT: o 263 LYS cc_start: 0.9270 (ttpp) cc_final: 0.8903 (ttpp) REVERT: p 32 GLU cc_start: 0.9383 (pt0) cc_final: 0.9040 (pt0) outliers start: 61 outliers final: 10 residues processed: 687 average time/residue: 1.1571 time to fit residues: 903.9618 Evaluate side-chains 629 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 600 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 308 GLU Chi-restraints excluded: chain S residue 374 ASN Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain b residue 308 GLU Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain k residue 374 ASN Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 362 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN D 360 ASN D 374 ASN E 220 HIS G 271 GLN G 284 ASN G 374 ASN I 30 ASN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 ASN M 263 GLN M 360 ASN M 374 ASN P 357 ASN P 374 ASN S 209 GLN V 374 ASN Y 360 ASN Y 374 ASN b 284 ASN b 374 ASN ** e 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 ASN h 263 GLN h 360 ASN h 374 ASN k 357 ASN n 209 GLN n 374 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.035585 restraints weight = 118133.010| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 3.17 r_work: 0.2341 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 39214 Z= 0.385 Angle : 0.661 9.934 53158 Z= 0.343 Chirality : 0.045 0.138 5796 Planarity : 0.005 0.052 7084 Dihedral : 4.283 14.331 5502 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.98 % Allowed : 17.84 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.12), residues: 4942 helix: 2.44 (0.19), residues: 798 sheet: 0.49 (0.17), residues: 938 loop : 0.25 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 259 TYR 0.021 0.002 TYR e 387 PHE 0.025 0.002 PHE K 195 TRP 0.010 0.001 TRP e 307 HIS 0.003 0.001 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00882 (39200) covalent geometry : angle 0.66149 (53130) SS BOND : bond 0.00072 ( 14) SS BOND : angle 0.45285 ( 28) hydrogen bonds : bond 0.03924 ( 1555) hydrogen bonds : angle 5.51991 ( 3993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 582 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 308 GLU cc_start: 0.8585 (mp0) cc_final: 0.8327 (mp0) REVERT: A 353 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8825 (mm-30) REVERT: A 357 ASN cc_start: 0.9100 (m-40) cc_final: 0.8675 (m110) REVERT: A 371 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8632 (mt-10) REVERT: A 374 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8861 (t0) REVERT: A 390 GLU cc_start: 0.8051 (pp20) cc_final: 0.7605 (pp20) REVERT: B 159 LYS cc_start: 0.8967 (mppt) cc_final: 0.8564 (mppt) REVERT: B 161 MET cc_start: 0.9348 (mmm) cc_final: 0.8785 (mmm) REVERT: B 263 LYS cc_start: 0.9290 (ttpp) cc_final: 0.8876 (ttpp) REVERT: D 276 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8594 (tm-30) REVERT: D 308 GLU cc_start: 0.8675 (mp0) cc_final: 0.8374 (mp0) REVERT: D 353 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8985 (mm-30) REVERT: D 357 ASN cc_start: 0.9076 (m-40) cc_final: 0.8811 (m110) REVERT: D 371 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8664 (mt-10) REVERT: D 390 GLU cc_start: 0.8143 (pp20) cc_final: 0.7789 (pp20) REVERT: E 145 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8925 (mp0) REVERT: E 159 LYS cc_start: 0.9067 (mppt) cc_final: 0.8662 (mppt) REVERT: E 161 MET cc_start: 0.9349 (mmm) cc_final: 0.8780 (mmm) REVERT: E 240 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8970 (mm-30) REVERT: F 30 ASN cc_start: 0.8215 (p0) cc_final: 0.6988 (p0) REVERT: F 32 GLU cc_start: 0.9311 (pt0) cc_final: 0.8848 (pm20) REVERT: G 276 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8548 (tm-30) REVERT: G 308 GLU cc_start: 0.8661 (mp0) cc_final: 0.8248 (mp0) REVERT: G 353 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8631 (mm-30) REVERT: G 357 ASN cc_start: 0.9157 (m-40) cc_final: 0.8606 (m110) REVERT: G 371 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8419 (mt-10) REVERT: G 390 GLU cc_start: 0.8754 (pt0) cc_final: 0.8426 (pp20) REVERT: H 137 GLU cc_start: 0.8431 (pm20) cc_final: 0.8164 (pm20) REVERT: H 145 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8806 (mp0) REVERT: H 159 LYS cc_start: 0.9028 (mppt) cc_final: 0.8752 (mppt) REVERT: H 161 MET cc_start: 0.9397 (mmm) cc_final: 0.8818 (mmm) REVERT: H 162 MET cc_start: 0.9627 (ptt) cc_final: 0.8803 (ptt) REVERT: H 263 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8603 (ttpp) REVERT: I 30 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7843 (p0) REVERT: I 32 GLU cc_start: 0.9307 (pt0) cc_final: 0.8855 (pm20) REVERT: J 185 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8736 (mm-30) REVERT: J 276 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8597 (tm-30) REVERT: J 308 GLU cc_start: 0.8448 (mp0) cc_final: 0.8199 (mp0) REVERT: J 353 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8877 (mm-30) REVERT: J 357 ASN cc_start: 0.9167 (m-40) cc_final: 0.8743 (m110) REVERT: J 390 GLU cc_start: 0.8065 (pp20) cc_final: 0.7651 (pp20) REVERT: K 145 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8841 (mp0) REVERT: K 159 LYS cc_start: 0.9031 (mppt) cc_final: 0.8642 (mppt) REVERT: K 161 MET cc_start: 0.9387 (mmm) cc_final: 0.8798 (mmm) REVERT: K 240 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8940 (mm-30) REVERT: M 276 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8604 (tm-30) REVERT: M 308 GLU cc_start: 0.8534 (mp0) cc_final: 0.8329 (mp0) REVERT: M 353 GLU cc_start: 0.9402 (tp30) cc_final: 0.9038 (tp30) REVERT: M 357 ASN cc_start: 0.9118 (m-40) cc_final: 0.8767 (m110) REVERT: M 371 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8655 (mt-10) REVERT: M 374 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8901 (t0) REVERT: M 390 GLU cc_start: 0.8039 (pp20) cc_final: 0.7620 (pp20) REVERT: N 141 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8592 (ttp80) REVERT: N 145 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: N 159 LYS cc_start: 0.9020 (mppt) cc_final: 0.8629 (mppt) REVERT: N 161 MET cc_start: 0.9400 (mmm) cc_final: 0.8935 (mmm) REVERT: P 276 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8583 (tm-30) REVERT: P 308 GLU cc_start: 0.8734 (mp0) cc_final: 0.8310 (mp0) REVERT: P 319 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9277 (mp) REVERT: P 390 GLU cc_start: 0.8021 (pp20) cc_final: 0.7461 (pp20) REVERT: Q 141 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8806 (tmm-80) REVERT: Q 145 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8955 (OUTLIER) REVERT: Q 159 LYS cc_start: 0.9060 (mppt) cc_final: 0.8709 (mppt) REVERT: Q 161 MET cc_start: 0.9398 (mmm) cc_final: 0.8852 (mmm) REVERT: S 276 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8577 (tm-30) REVERT: S 308 GLU cc_start: 0.8593 (mp0) cc_final: 0.8356 (mp0) REVERT: S 353 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8803 (mm-30) REVERT: S 357 ASN cc_start: 0.9251 (m-40) cc_final: 0.8726 (m110) REVERT: S 390 GLU cc_start: 0.8001 (pp20) cc_final: 0.7569 (pp20) REVERT: T 137 GLU cc_start: 0.8229 (pm20) cc_final: 0.7806 (pm20) REVERT: T 145 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: T 159 LYS cc_start: 0.8952 (mppt) cc_final: 0.8576 (mppt) REVERT: T 202 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9150 (mt-10) REVERT: T 259 ARG cc_start: 0.9058 (ttm110) cc_final: 0.8723 (ttm-80) REVERT: T 263 LYS cc_start: 0.9287 (ttpp) cc_final: 0.8849 (ttpp) REVERT: V 276 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8475 (tm-30) REVERT: V 308 GLU cc_start: 0.8598 (mp0) cc_final: 0.8309 (mp0) REVERT: V 353 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8831 (mm-30) REVERT: V 357 ASN cc_start: 0.9102 (m-40) cc_final: 0.8686 (m110) REVERT: V 374 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8865 (t0) REVERT: V 390 GLU cc_start: 0.8039 (pp20) cc_final: 0.7571 (pp20) REVERT: W 141 ARG cc_start: 0.8989 (ttp80) cc_final: 0.8689 (ttp80) REVERT: W 159 LYS cc_start: 0.8988 (mppt) cc_final: 0.8587 (mppt) REVERT: W 161 MET cc_start: 0.9352 (mmm) cc_final: 0.8804 (mmm) REVERT: W 263 LYS cc_start: 0.9290 (ttpp) cc_final: 0.8865 (ttpp) REVERT: Y 276 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8600 (tm-30) REVERT: Y 308 GLU cc_start: 0.8661 (mp0) cc_final: 0.8343 (mp0) REVERT: Y 353 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8979 (mm-30) REVERT: Y 357 ASN cc_start: 0.9100 (m-40) cc_final: 0.8836 (m110) REVERT: Y 371 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8657 (mt-10) REVERT: Y 390 GLU cc_start: 0.8167 (pp20) cc_final: 0.7850 (pp20) REVERT: Z 141 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8523 (ttp80) REVERT: Z 145 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: Z 159 LYS cc_start: 0.9081 (mppt) cc_final: 0.8684 (mppt) REVERT: Z 161 MET cc_start: 0.9348 (mmm) cc_final: 0.8793 (mmm) REVERT: Z 240 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8974 (mm-30) REVERT: a 32 GLU cc_start: 0.9324 (pt0) cc_final: 0.8910 (pm20) REVERT: b 276 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8536 (tm-30) REVERT: b 308 GLU cc_start: 0.8669 (mp0) cc_final: 0.8254 (mp0) REVERT: b 353 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8623 (mm-30) REVERT: b 357 ASN cc_start: 0.9160 (m-40) cc_final: 0.8605 (m110) REVERT: b 371 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8407 (mt-10) REVERT: c 145 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8742 (mp0) REVERT: c 159 LYS cc_start: 0.8992 (mppt) cc_final: 0.8690 (mppt) REVERT: c 161 MET cc_start: 0.9390 (mmm) cc_final: 0.8761 (mmm) REVERT: c 162 MET cc_start: 0.9666 (ptt) cc_final: 0.8812 (ptp) REVERT: c 263 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8604 (ttpp) REVERT: d 32 GLU cc_start: 0.9385 (pt0) cc_final: 0.8832 (pm20) REVERT: e 185 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8727 (mm-30) REVERT: e 276 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8599 (tm-30) REVERT: e 308 GLU cc_start: 0.8447 (mp0) cc_final: 0.8193 (mp0) REVERT: e 353 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8849 (mm-30) REVERT: e 357 ASN cc_start: 0.9178 (m-40) cc_final: 0.8742 (m110) REVERT: e 390 GLU cc_start: 0.8045 (pp20) cc_final: 0.7658 (pp20) REVERT: f 141 ARG cc_start: 0.8922 (ttp80) cc_final: 0.8567 (ttp80) REVERT: f 145 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: f 159 LYS cc_start: 0.8964 (mppt) cc_final: 0.8581 (mppt) REVERT: f 161 MET cc_start: 0.9371 (mmm) cc_final: 0.8943 (mmm) REVERT: f 202 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9112 (mt-10) REVERT: f 240 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8911 (mm-30) REVERT: h 276 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8621 (tm-30) REVERT: h 308 GLU cc_start: 0.8534 (mp0) cc_final: 0.8331 (mp0) REVERT: h 353 GLU cc_start: 0.9425 (tp30) cc_final: 0.9036 (tp30) REVERT: h 357 ASN cc_start: 0.9150 (m-40) cc_final: 0.8793 (m110) REVERT: h 371 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8652 (mt-10) REVERT: h 374 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8927 (t0) REVERT: i 159 LYS cc_start: 0.9012 (mppt) cc_final: 0.8616 (mppt) REVERT: i 161 MET cc_start: 0.9386 (mmm) cc_final: 0.8947 (mmm) REVERT: k 276 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8592 (tm-30) REVERT: k 308 GLU cc_start: 0.8715 (mp0) cc_final: 0.8316 (mp0) REVERT: k 390 GLU cc_start: 0.8091 (pp20) cc_final: 0.7602 (pp20) REVERT: l 141 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8813 (tmm-80) REVERT: l 145 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8938 (OUTLIER) REVERT: l 159 LYS cc_start: 0.9064 (mppt) cc_final: 0.8709 (mppt) REVERT: l 161 MET cc_start: 0.9395 (mmm) cc_final: 0.8842 (mmm) REVERT: n 276 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8581 (tm-30) REVERT: n 308 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: n 353 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8746 (tp30) REVERT: n 357 ASN cc_start: 0.9248 (m-40) cc_final: 0.8721 (m110) REVERT: n 374 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8895 (t0) REVERT: n 390 GLU cc_start: 0.7994 (pp20) cc_final: 0.7641 (pp20) REVERT: o 137 GLU cc_start: 0.8377 (pm20) cc_final: 0.7988 (pm20) REVERT: o 141 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8538 (ttp80) REVERT: o 145 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: o 159 LYS cc_start: 0.8941 (mppt) cc_final: 0.8575 (mppt) REVERT: o 202 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9151 (mt-10) REVERT: o 263 LYS cc_start: 0.9289 (ttpp) cc_final: 0.8857 (ttpp) outliers start: 80 outliers final: 15 residues processed: 637 average time/residue: 1.1269 time to fit residues: 815.2447 Evaluate side-chains 585 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 552 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 374 ASN Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 263 LYS Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain h residue 374 ASN Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain n residue 374 ASN Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 240 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 471 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 355 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 465 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 476 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN D 360 ASN D 374 ASN G 271 GLN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 GLN J 374 ASN M 188 GLN M 360 ASN M 374 ASN V 374 ASN Y 360 ASN Y 374 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 188 GLN e 374 ASN h 188 GLN h 360 ASN h 374 ASN k 357 ASN k 374 ASN ** n 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 374 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.050549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.036911 restraints weight = 116416.165| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 3.18 r_work: 0.2382 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39214 Z= 0.165 Angle : 0.580 10.870 53158 Z= 0.301 Chirality : 0.043 0.140 5796 Planarity : 0.004 0.057 7084 Dihedral : 4.091 13.311 5502 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.66 % Allowed : 18.19 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.12), residues: 4942 helix: 2.35 (0.19), residues: 798 sheet: 0.46 (0.17), residues: 938 loop : 0.28 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 141 TYR 0.014 0.001 TYR e 387 PHE 0.023 0.001 PHE E 195 TRP 0.008 0.001 TRP Y 307 HIS 0.001 0.000 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00382 (39200) covalent geometry : angle 0.58006 (53130) SS BOND : bond 0.00118 ( 14) SS BOND : angle 0.31194 ( 28) hydrogen bonds : bond 0.03294 ( 1555) hydrogen bonds : angle 5.44488 ( 3993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 611 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 308 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: A 353 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8805 (mm-30) REVERT: A 357 ASN cc_start: 0.9057 (m-40) cc_final: 0.8659 (m110) REVERT: A 390 GLU cc_start: 0.8016 (pp20) cc_final: 0.7654 (pp20) REVERT: B 141 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8436 (ttp80) REVERT: B 145 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8835 (mp0) REVERT: B 159 LYS cc_start: 0.8983 (mppt) cc_final: 0.8580 (mppt) REVERT: B 161 MET cc_start: 0.9371 (mmm) cc_final: 0.8657 (mmm) REVERT: B 263 LYS cc_start: 0.9314 (ttpp) cc_final: 0.8929 (ttpp) REVERT: C 24 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.8708 (ttpt) REVERT: D 276 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8568 (tm-30) REVERT: D 308 GLU cc_start: 0.8596 (mp0) cc_final: 0.8249 (mp0) REVERT: D 353 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8999 (mm-30) REVERT: D 357 ASN cc_start: 0.9053 (m-40) cc_final: 0.8807 (m110) REVERT: D 371 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: D 390 GLU cc_start: 0.8182 (pp20) cc_final: 0.7793 (pp20) REVERT: E 141 ARG cc_start: 0.8814 (tmm-80) cc_final: 0.8337 (ttp80) REVERT: E 145 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8761 (mp0) REVERT: E 159 LYS cc_start: 0.9047 (mppt) cc_final: 0.8654 (mppt) REVERT: E 161 MET cc_start: 0.9368 (mmm) cc_final: 0.8766 (mmm) REVERT: G 276 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8545 (tm-30) REVERT: G 308 GLU cc_start: 0.8649 (mp0) cc_final: 0.8216 (mp0) REVERT: G 371 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8398 (mt-10) REVERT: G 390 GLU cc_start: 0.8807 (pt0) cc_final: 0.8150 (pp20) REVERT: H 137 GLU cc_start: 0.8374 (pm20) cc_final: 0.8100 (pm20) REVERT: H 145 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: H 159 LYS cc_start: 0.8988 (mppt) cc_final: 0.8679 (mppt) REVERT: H 161 MET cc_start: 0.9416 (mmm) cc_final: 0.8777 (mmm) REVERT: H 162 MET cc_start: 0.9653 (ptt) cc_final: 0.8765 (ptt) REVERT: H 263 LYS cc_start: 0.9275 (ttpp) cc_final: 0.9042 (ttpp) REVERT: I 32 GLU cc_start: 0.9278 (pt0) cc_final: 0.8886 (pm20) REVERT: J 185 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (mm-30) REVERT: J 276 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8564 (tm-30) REVERT: J 308 GLU cc_start: 0.8485 (mp0) cc_final: 0.8206 (mp0) REVERT: J 353 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8743 (mm-30) REVERT: J 357 ASN cc_start: 0.9125 (m-40) cc_final: 0.8684 (m110) REVERT: J 390 GLU cc_start: 0.8025 (pp20) cc_final: 0.7655 (pp20) REVERT: K 141 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8609 (tmm-80) REVERT: K 145 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8773 (mp0) REVERT: K 159 LYS cc_start: 0.9013 (mppt) cc_final: 0.8647 (mppt) REVERT: K 161 MET cc_start: 0.9403 (mmm) cc_final: 0.8808 (mmm) REVERT: K 240 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8979 (mm-30) REVERT: M 276 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8585 (tm-30) REVERT: M 353 GLU cc_start: 0.9405 (tp30) cc_final: 0.9017 (tp30) REVERT: M 357 ASN cc_start: 0.9103 (m-40) cc_final: 0.8757 (m110) REVERT: M 371 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8631 (mt-10) REVERT: M 390 GLU cc_start: 0.8052 (pp20) cc_final: 0.7597 (pp20) REVERT: N 141 ARG cc_start: 0.9002 (ttp80) cc_final: 0.8552 (ttp80) REVERT: N 145 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8495 (mp0) REVERT: N 159 LYS cc_start: 0.9013 (mppt) cc_final: 0.8650 (mppt) REVERT: N 161 MET cc_start: 0.9393 (mmm) cc_final: 0.8924 (mmm) REVERT: P 185 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8484 (mm-30) REVERT: P 276 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8577 (tm-30) REVERT: P 308 GLU cc_start: 0.8658 (mp0) cc_final: 0.8245 (mp0) REVERT: P 371 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8445 (mt-10) REVERT: P 390 GLU cc_start: 0.7992 (pp20) cc_final: 0.7410 (pp20) REVERT: Q 141 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8594 (ttp80) REVERT: Q 145 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8738 (mp0) REVERT: Q 159 LYS cc_start: 0.9056 (mppt) cc_final: 0.8657 (mppt) REVERT: Q 161 MET cc_start: 0.9361 (mmm) cc_final: 0.8890 (mmm) REVERT: S 276 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8582 (tm-30) REVERT: S 308 GLU cc_start: 0.8565 (mp0) cc_final: 0.8283 (mp0) REVERT: S 353 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8666 (tp30) REVERT: S 357 ASN cc_start: 0.9217 (m-40) cc_final: 0.8656 (m110) REVERT: S 390 GLU cc_start: 0.8053 (pp20) cc_final: 0.7586 (pp20) REVERT: T 141 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8574 (ttp80) REVERT: T 145 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: T 159 LYS cc_start: 0.8947 (mppt) cc_final: 0.8574 (mppt) REVERT: T 202 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9150 (mt-10) REVERT: T 227 MET cc_start: 0.9530 (tpp) cc_final: 0.9134 (tpp) REVERT: T 259 ARG cc_start: 0.8996 (ttm110) cc_final: 0.8648 (ttm-80) REVERT: T 263 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9110 (ttpp) REVERT: V 276 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8481 (tm-30) REVERT: V 308 GLU cc_start: 0.8586 (mp0) cc_final: 0.8279 (mp0) REVERT: V 353 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8803 (mm-30) REVERT: V 357 ASN cc_start: 0.9063 (m-40) cc_final: 0.8658 (m110) REVERT: V 390 GLU cc_start: 0.8007 (pp20) cc_final: 0.7585 (pp20) REVERT: W 141 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8631 (tmm-80) REVERT: W 145 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9032 (mp0) REVERT: W 159 LYS cc_start: 0.8987 (mppt) cc_final: 0.8579 (mppt) REVERT: W 161 MET cc_start: 0.9371 (mmm) cc_final: 0.8672 (mmm) REVERT: W 263 LYS cc_start: 0.9323 (ttpp) cc_final: 0.8926 (ttpp) REVERT: Y 276 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8576 (tm-30) REVERT: Y 308 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: Y 353 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9023 (mm-30) REVERT: Y 357 ASN cc_start: 0.9080 (m-40) cc_final: 0.8835 (m110) REVERT: Y 371 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: Y 390 GLU cc_start: 0.8211 (pp20) cc_final: 0.7864 (pp20) REVERT: Z 141 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8576 (ttp80) REVERT: Z 145 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: Z 159 LYS cc_start: 0.9059 (mppt) cc_final: 0.8663 (mppt) REVERT: Z 161 MET cc_start: 0.9380 (mmm) cc_final: 0.8782 (mmm) REVERT: Z 162 MET cc_start: 0.9411 (ptt) cc_final: 0.9101 (ptt) REVERT: a 30 ASN cc_start: 0.8222 (p0) cc_final: 0.7628 (p0) REVERT: a 32 GLU cc_start: 0.9314 (pt0) cc_final: 0.8868 (pm20) REVERT: b 276 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8544 (tm-30) REVERT: b 308 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: b 353 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8618 (mm-30) REVERT: b 357 ASN cc_start: 0.9137 (m-40) cc_final: 0.8573 (m110) REVERT: b 371 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8431 (mt-10) REVERT: c 159 LYS cc_start: 0.9015 (mppt) cc_final: 0.8725 (mppt) REVERT: c 161 MET cc_start: 0.9398 (mmm) cc_final: 0.8288 (mmm) REVERT: c 162 MET cc_start: 0.9652 (ptt) cc_final: 0.9136 (ptp) REVERT: c 263 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9043 (ttpp) REVERT: d 32 GLU cc_start: 0.9370 (pt0) cc_final: 0.8751 (pm20) REVERT: e 185 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8688 (mm-30) REVERT: e 276 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8562 (tm-30) REVERT: e 308 GLU cc_start: 0.8396 (mp0) cc_final: 0.8115 (mp0) REVERT: e 353 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8717 (mm-30) REVERT: e 357 ASN cc_start: 0.9148 (m-40) cc_final: 0.8673 (m110) REVERT: e 390 GLU cc_start: 0.8012 (pp20) cc_final: 0.7626 (pp20) REVERT: f 141 ARG cc_start: 0.8900 (ttp80) cc_final: 0.8564 (ttp80) REVERT: f 145 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: f 159 LYS cc_start: 0.8958 (mppt) cc_final: 0.8610 (mppt) REVERT: f 161 MET cc_start: 0.9378 (mmm) cc_final: 0.8923 (mmm) REVERT: f 240 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8954 (mm-30) REVERT: h 276 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8589 (tm-30) REVERT: h 353 GLU cc_start: 0.9412 (tp30) cc_final: 0.9008 (tp30) REVERT: h 357 ASN cc_start: 0.9106 (m-40) cc_final: 0.8766 (m110) REVERT: h 371 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8637 (mt-10) REVERT: i 141 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8500 (ttp80) REVERT: i 145 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: i 159 LYS cc_start: 0.9004 (mppt) cc_final: 0.8642 (mppt) REVERT: i 161 MET cc_start: 0.9384 (mmm) cc_final: 0.8941 (mmm) REVERT: j 32 GLU cc_start: 0.9390 (pt0) cc_final: 0.9100 (pt0) REVERT: k 276 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8576 (tm-30) REVERT: k 308 GLU cc_start: 0.8664 (mp0) cc_final: 0.8237 (mp0) REVERT: k 371 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8409 (mt-10) REVERT: k 390 GLU cc_start: 0.8167 (pp20) cc_final: 0.7552 (pp20) REVERT: l 145 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8998 (mp0) REVERT: l 159 LYS cc_start: 0.9055 (mppt) cc_final: 0.8661 (mppt) REVERT: l 161 MET cc_start: 0.9356 (mmm) cc_final: 0.8902 (mmm) REVERT: n 276 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8582 (tm-30) REVERT: n 308 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: n 353 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8632 (tp30) REVERT: n 357 ASN cc_start: 0.9215 (m-40) cc_final: 0.8642 (m110) REVERT: n 390 GLU cc_start: 0.8055 (pp20) cc_final: 0.7604 (pp20) REVERT: o 145 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: o 159 LYS cc_start: 0.8936 (mppt) cc_final: 0.8538 (mppt) REVERT: o 259 ARG cc_start: 0.9040 (ttm-80) cc_final: 0.8578 (ttm-80) REVERT: o 263 LYS cc_start: 0.9313 (ttpp) cc_final: 0.9111 (ttpp) outliers start: 67 outliers final: 15 residues processed: 650 average time/residue: 1.1108 time to fit residues: 821.0780 Evaluate side-chains 620 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 585 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain N residue 225 LYS Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain W residue 145 GLU Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain b residue 308 GLU Chi-restraints excluded: chain c residue 263 LYS Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain i residue 225 LYS Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 13 optimal weight: 7.9990 chunk 190 optimal weight: 30.0000 chunk 371 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 337 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 464 optimal weight: 2.9990 chunk 322 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN D 374 ASN G 374 ASN I 30 ASN J 374 ASN M 263 GLN M 360 ASN M 374 ASN P 212 GLN S 284 ASN V 374 ASN Y 360 ASN Y 374 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 ASN h 360 ASN h 374 ASN k 212 GLN k 357 ASN m 25 GLN n 284 ASN n 374 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.036724 restraints weight = 117034.505| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 3.19 r_work: 0.2375 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 39214 Z= 0.216 Angle : 0.612 11.323 53158 Z= 0.316 Chirality : 0.043 0.139 5796 Planarity : 0.004 0.063 7084 Dihedral : 4.053 15.121 5502 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.63 % Allowed : 18.71 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.12), residues: 4942 helix: 2.34 (0.19), residues: 798 sheet: 0.44 (0.17), residues: 938 loop : 0.28 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 141 TYR 0.022 0.001 TYR S 387 PHE 0.023 0.001 PHE E 195 TRP 0.008 0.001 TRP Y 307 HIS 0.001 0.000 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00502 (39200) covalent geometry : angle 0.61240 (53130) SS BOND : bond 0.00071 ( 14) SS BOND : angle 0.34005 ( 28) hydrogen bonds : bond 0.03380 ( 1555) hydrogen bonds : angle 5.38824 ( 3993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 608 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8448 (tm-30) REVERT: A 308 GLU cc_start: 0.8558 (mp0) cc_final: 0.8251 (mp0) REVERT: A 353 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8806 (mm-30) REVERT: A 357 ASN cc_start: 0.9045 (m-40) cc_final: 0.8640 (m110) REVERT: A 374 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8887 (t0) REVERT: A 390 GLU cc_start: 0.8037 (pp20) cc_final: 0.7751 (pp20) REVERT: B 136 ARG cc_start: 0.8264 (pmm150) cc_final: 0.7885 (pmm-80) REVERT: B 137 GLU cc_start: 0.8396 (pm20) cc_final: 0.8189 (pm20) REVERT: B 141 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8484 (ttp80) REVERT: B 145 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: B 159 LYS cc_start: 0.8994 (mppt) cc_final: 0.8623 (mppt) REVERT: B 161 MET cc_start: 0.9345 (mmm) cc_final: 0.8575 (mmm) REVERT: B 227 MET cc_start: 0.9356 (tpt) cc_final: 0.9147 (tpt) REVERT: B 263 LYS cc_start: 0.9308 (ttpp) cc_final: 0.8922 (ttpp) REVERT: C 24 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.8687 (ttpt) REVERT: D 276 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8580 (tm-30) REVERT: D 308 GLU cc_start: 0.8664 (mp0) cc_final: 0.8337 (mp0) REVERT: D 353 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8995 (mm-30) REVERT: D 357 ASN cc_start: 0.9051 (m-40) cc_final: 0.8779 (m110) REVERT: D 371 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: D 390 GLU cc_start: 0.8283 (pp20) cc_final: 0.7822 (pp20) REVERT: E 145 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8986 (mp0) REVERT: E 159 LYS cc_start: 0.9052 (mppt) cc_final: 0.8605 (mppt) REVERT: E 161 MET cc_start: 0.9303 (mmm) cc_final: 0.8749 (mmm) REVERT: E 162 MET cc_start: 0.9406 (ptt) cc_final: 0.9096 (ptt) REVERT: F 30 ASN cc_start: 0.8205 (p0) cc_final: 0.6823 (p0) REVERT: F 32 GLU cc_start: 0.9310 (pt0) cc_final: 0.8825 (pm20) REVERT: G 276 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8517 (tm-30) REVERT: G 308 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: G 371 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8364 (mt-10) REVERT: G 390 GLU cc_start: 0.8788 (pt0) cc_final: 0.8430 (pp20) REVERT: H 137 GLU cc_start: 0.8297 (pm20) cc_final: 0.8027 (pm20) REVERT: H 159 LYS cc_start: 0.9001 (mppt) cc_final: 0.8665 (mppt) REVERT: H 161 MET cc_start: 0.9378 (mmm) cc_final: 0.8840 (mmm) REVERT: H 162 MET cc_start: 0.9649 (ptt) cc_final: 0.8844 (ptt) REVERT: H 263 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.9015 (ttpp) REVERT: I 30 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (p0) REVERT: I 32 GLU cc_start: 0.9292 (pt0) cc_final: 0.8865 (pm20) REVERT: J 185 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8643 (mm-30) REVERT: J 276 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8559 (tm-30) REVERT: J 308 GLU cc_start: 0.8481 (mp0) cc_final: 0.8220 (mp0) REVERT: J 353 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8844 (mm-30) REVERT: J 357 ASN cc_start: 0.9127 (m-40) cc_final: 0.8693 (m110) REVERT: J 390 GLU cc_start: 0.8129 (pp20) cc_final: 0.7622 (pp20) REVERT: K 145 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8738 (mp0) REVERT: K 159 LYS cc_start: 0.9015 (mppt) cc_final: 0.8612 (mppt) REVERT: K 161 MET cc_start: 0.9391 (mmm) cc_final: 0.8800 (mmm) REVERT: K 240 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8990 (mm-30) REVERT: M 276 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8562 (tm-30) REVERT: M 353 GLU cc_start: 0.9400 (tp30) cc_final: 0.9015 (tp30) REVERT: M 357 ASN cc_start: 0.9100 (m-40) cc_final: 0.8769 (m110) REVERT: M 371 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8627 (mt-10) REVERT: M 374 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8907 (t0) REVERT: M 390 GLU cc_start: 0.8200 (pp20) cc_final: 0.7755 (pp20) REVERT: N 141 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8561 (ttp80) REVERT: N 145 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: N 159 LYS cc_start: 0.9030 (mppt) cc_final: 0.8619 (mppt) REVERT: N 161 MET cc_start: 0.9368 (mmm) cc_final: 0.8869 (mmm) REVERT: P 185 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8567 (mm-30) REVERT: P 276 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8566 (tm-30) REVERT: P 308 GLU cc_start: 0.8716 (mp0) cc_final: 0.8292 (mp0) REVERT: P 371 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8411 (mt-10) REVERT: P 390 GLU cc_start: 0.7983 (pp20) cc_final: 0.7381 (pp20) REVERT: Q 145 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8981 (mp0) REVERT: Q 159 LYS cc_start: 0.9058 (mppt) cc_final: 0.8646 (mppt) REVERT: Q 161 MET cc_start: 0.9319 (mmm) cc_final: 0.8909 (mmm) REVERT: S 276 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8551 (tm-30) REVERT: S 308 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: S 353 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8664 (tp30) REVERT: S 357 ASN cc_start: 0.9211 (m-40) cc_final: 0.8635 (m110) REVERT: S 390 GLU cc_start: 0.8100 (pp20) cc_final: 0.7585 (pp20) REVERT: T 145 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8827 (mp0) REVERT: T 159 LYS cc_start: 0.8958 (mppt) cc_final: 0.8542 (mppt) REVERT: T 259 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8639 (ttm-80) REVERT: T 263 LYS cc_start: 0.9307 (ttpp) cc_final: 0.8938 (ttpp) REVERT: V 276 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8468 (tm-30) REVERT: V 308 GLU cc_start: 0.8572 (mp0) cc_final: 0.8269 (mp0) REVERT: V 353 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8805 (mm-30) REVERT: V 357 ASN cc_start: 0.9060 (m-40) cc_final: 0.8661 (m110) REVERT: V 374 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8853 (t0) REVERT: V 390 GLU cc_start: 0.8067 (pp20) cc_final: 0.7758 (pp20) REVERT: W 141 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8610 (tmm-80) REVERT: W 145 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: W 159 LYS cc_start: 0.9000 (mppt) cc_final: 0.8625 (mppt) REVERT: W 161 MET cc_start: 0.9347 (mmm) cc_final: 0.8592 (mmm) REVERT: W 227 MET cc_start: 0.9350 (tpt) cc_final: 0.9139 (tpt) REVERT: W 263 LYS cc_start: 0.9299 (ttpp) cc_final: 0.8798 (ttpp) REVERT: Y 276 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8577 (tm-30) REVERT: Y 308 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: Y 353 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9007 (mm-30) REVERT: Y 357 ASN cc_start: 0.9064 (m-40) cc_final: 0.8812 (m110) REVERT: Y 371 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: Y 390 GLU cc_start: 0.8287 (pp20) cc_final: 0.7792 (pp20) REVERT: Z 141 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8560 (ttp80) REVERT: Z 145 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: Z 159 LYS cc_start: 0.9051 (mppt) cc_final: 0.8614 (mppt) REVERT: Z 161 MET cc_start: 0.9314 (mmm) cc_final: 0.8761 (mmm) REVERT: a 30 ASN cc_start: 0.8236 (p0) cc_final: 0.7641 (p0) REVERT: a 32 GLU cc_start: 0.9326 (pt0) cc_final: 0.8894 (pm20) REVERT: b 276 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8520 (tm-30) REVERT: b 308 GLU cc_start: 0.8707 (mp0) cc_final: 0.8287 (mp0) REVERT: b 371 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8424 (mt-10) REVERT: c 141 ARG cc_start: 0.8780 (tmm-80) cc_final: 0.8546 (ttp80) REVERT: c 145 GLU cc_start: 0.8974 (mp0) cc_final: 0.8690 (mp0) REVERT: c 159 LYS cc_start: 0.8984 (mppt) cc_final: 0.8669 (mppt) REVERT: c 161 MET cc_start: 0.9369 (mmm) cc_final: 0.8706 (mmm) REVERT: c 162 MET cc_start: 0.9653 (ptt) cc_final: 0.9341 (ptp) REVERT: c 263 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9032 (ttpp) REVERT: e 185 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: e 276 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8559 (tm-30) REVERT: e 308 GLU cc_start: 0.8409 (mp0) cc_final: 0.8183 (mp0) REVERT: e 353 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8850 (mm-30) REVERT: e 357 ASN cc_start: 0.9141 (m-40) cc_final: 0.8706 (m110) REVERT: e 390 GLU cc_start: 0.8155 (pp20) cc_final: 0.7643 (pp20) REVERT: f 145 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: f 159 LYS cc_start: 0.8954 (mppt) cc_final: 0.8584 (mppt) REVERT: f 161 MET cc_start: 0.9376 (mmm) cc_final: 0.8922 (mmm) REVERT: f 240 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8965 (mm-30) REVERT: h 276 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8568 (tm-30) REVERT: h 353 GLU cc_start: 0.9415 (tp30) cc_final: 0.8994 (tp30) REVERT: h 357 ASN cc_start: 0.9112 (m-40) cc_final: 0.8754 (m110) REVERT: h 371 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8624 (mt-10) REVERT: h 374 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8894 (t0) REVERT: i 141 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8443 (ttp80) REVERT: i 145 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: i 159 LYS cc_start: 0.9025 (mppt) cc_final: 0.8615 (mppt) REVERT: i 161 MET cc_start: 0.9388 (mmm) cc_final: 0.8901 (mmm) REVERT: k 276 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8590 (tm-30) REVERT: k 308 GLU cc_start: 0.8655 (mp0) cc_final: 0.8243 (mp0) REVERT: k 371 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8429 (mt-10) REVERT: k 390 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: l 141 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8724 (tmm-80) REVERT: l 145 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8947 (mp0) REVERT: l 159 LYS cc_start: 0.9066 (mppt) cc_final: 0.8660 (mppt) REVERT: l 161 MET cc_start: 0.9329 (mmm) cc_final: 0.8923 (mmm) REVERT: n 276 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8567 (tm-30) REVERT: n 308 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: n 353 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8630 (tp30) REVERT: n 357 ASN cc_start: 0.9206 (m-40) cc_final: 0.8632 (m110) REVERT: n 374 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8882 (t0) REVERT: n 390 GLU cc_start: 0.8092 (pp20) cc_final: 0.7654 (pp20) REVERT: o 141 ARG cc_start: 0.8750 (tmm-80) cc_final: 0.8439 (ttp80) REVERT: o 145 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: o 159 LYS cc_start: 0.8959 (mppt) cc_final: 0.8512 (mppt) REVERT: o 202 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9081 (mt-10) REVERT: o 227 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9045 (tpp) REVERT: o 259 ARG cc_start: 0.9062 (ttm-80) cc_final: 0.8622 (ttm-80) REVERT: o 263 LYS cc_start: 0.9304 (ttpp) cc_final: 0.8935 (ttpp) outliers start: 66 outliers final: 14 residues processed: 644 average time/residue: 1.1373 time to fit residues: 834.4757 Evaluate side-chains 630 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 588 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 308 GLU Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain V residue 374 ASN Chi-restraints excluded: chain W residue 145 GLU Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 263 LYS Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain h residue 374 ASN Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain k residue 390 GLU Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain n residue 374 ASN Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 227 MET Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 130 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 427 optimal weight: 9.9990 chunk 384 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 ASN I 30 ASN J 374 ASN M 263 GLN M 360 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 188 GLN V 374 ASN Y 374 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 ASN h 360 ASN ** h 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 357 ASN ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.036638 restraints weight = 117018.804| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 3.19 r_work: 0.2374 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 39214 Z= 0.224 Angle : 0.619 12.503 53158 Z= 0.320 Chirality : 0.044 0.145 5796 Planarity : 0.004 0.052 7084 Dihedral : 4.046 15.699 5502 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 19.20 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.12), residues: 4942 helix: 2.34 (0.19), residues: 798 sheet: 0.47 (0.17), residues: 938 loop : 0.30 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG f 141 TYR 0.025 0.001 TYR n 387 PHE 0.022 0.001 PHE l 195 TRP 0.009 0.001 TRP D 301 HIS 0.001 0.000 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00520 (39200) covalent geometry : angle 0.61926 (53130) SS BOND : bond 0.00105 ( 14) SS BOND : angle 0.33395 ( 28) hydrogen bonds : bond 0.03371 ( 1555) hydrogen bonds : angle 5.36878 ( 3993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 594 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 308 GLU cc_start: 0.8570 (mp0) cc_final: 0.8263 (mp0) REVERT: A 353 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8796 (mm-30) REVERT: A 357 ASN cc_start: 0.9048 (m-40) cc_final: 0.8638 (m110) REVERT: A 374 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8853 (t0) REVERT: A 390 GLU cc_start: 0.8051 (pp20) cc_final: 0.7682 (pp20) REVERT: B 136 ARG cc_start: 0.8268 (pmm150) cc_final: 0.7946 (pmm-80) REVERT: B 137 GLU cc_start: 0.8335 (pm20) cc_final: 0.8071 (pm20) REVERT: B 141 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8662 (tmm-80) REVERT: B 145 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9027 (mp0) REVERT: B 159 LYS cc_start: 0.9001 (mppt) cc_final: 0.8624 (mppt) REVERT: B 161 MET cc_start: 0.9339 (mmm) cc_final: 0.8893 (mmm) REVERT: B 263 LYS cc_start: 0.9304 (ttpp) cc_final: 0.8809 (ttpp) REVERT: C 24 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8720 (ttpt) REVERT: D 276 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8558 (tm-30) REVERT: D 308 GLU cc_start: 0.8666 (mp0) cc_final: 0.8340 (mp0) REVERT: D 353 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8995 (mm-30) REVERT: D 357 ASN cc_start: 0.9025 (m-40) cc_final: 0.8760 (m110) REVERT: D 371 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: D 390 GLU cc_start: 0.8283 (pp20) cc_final: 0.7952 (pp20) REVERT: E 141 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8457 (tmm-80) REVERT: E 145 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8952 (mp0) REVERT: E 159 LYS cc_start: 0.9048 (mppt) cc_final: 0.8628 (mppt) REVERT: E 161 MET cc_start: 0.9316 (mmm) cc_final: 0.8753 (mmm) REVERT: F 30 ASN cc_start: 0.8197 (p0) cc_final: 0.7866 (p0) REVERT: G 276 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8519 (tm-30) REVERT: G 308 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: G 371 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8367 (mt-10) REVERT: G 390 GLU cc_start: 0.8831 (pt0) cc_final: 0.8306 (pp20) REVERT: H 137 GLU cc_start: 0.8368 (pm20) cc_final: 0.8148 (pm20) REVERT: H 141 ARG cc_start: 0.8722 (tmm-80) cc_final: 0.8394 (ttp80) REVERT: H 145 GLU cc_start: 0.8977 (mp0) cc_final: 0.8707 (mp0) REVERT: H 159 LYS cc_start: 0.9003 (mppt) cc_final: 0.8631 (mppt) REVERT: H 161 MET cc_start: 0.9391 (mmm) cc_final: 0.8467 (mmm) REVERT: H 162 MET cc_start: 0.9650 (ptt) cc_final: 0.8872 (ptt) REVERT: H 202 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9163 (mt-10) REVERT: H 263 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.9004 (ttpp) REVERT: I 30 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7863 (p0) REVERT: I 32 GLU cc_start: 0.9305 (pt0) cc_final: 0.8840 (pm20) REVERT: J 185 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8662 (mm-30) REVERT: J 276 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8618 (tm-30) REVERT: J 308 GLU cc_start: 0.8482 (mp0) cc_final: 0.8215 (mp0) REVERT: J 353 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8842 (mm-30) REVERT: J 357 ASN cc_start: 0.9128 (m-40) cc_final: 0.8694 (m110) REVERT: J 390 GLU cc_start: 0.8178 (pp20) cc_final: 0.7765 (pp20) REVERT: K 141 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8405 (ttp80) REVERT: K 145 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: K 159 LYS cc_start: 0.9019 (mppt) cc_final: 0.8622 (mppt) REVERT: K 161 MET cc_start: 0.9385 (mmm) cc_final: 0.8788 (mmm) REVERT: K 240 GLU cc_start: 0.9213 (mm-30) cc_final: 0.9005 (mm-30) REVERT: K 263 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8748 (ttpp) REVERT: M 276 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8557 (tm-30) REVERT: M 353 GLU cc_start: 0.9399 (tp30) cc_final: 0.9017 (tp30) REVERT: M 357 ASN cc_start: 0.9097 (m-40) cc_final: 0.8784 (m110) REVERT: M 371 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8648 (mt-10) REVERT: M 374 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8760 (t0) REVERT: M 390 GLU cc_start: 0.8187 (pp20) cc_final: 0.7749 (pp20) REVERT: N 145 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8722 (mp0) REVERT: N 149 GLU cc_start: 0.8968 (pp20) cc_final: 0.8516 (pp20) REVERT: N 159 LYS cc_start: 0.9046 (mppt) cc_final: 0.8682 (mppt) REVERT: N 161 MET cc_start: 0.9347 (mmm) cc_final: 0.8853 (mmm) REVERT: P 185 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8561 (mm-30) REVERT: P 276 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8573 (tm-30) REVERT: P 308 GLU cc_start: 0.8764 (mp0) cc_final: 0.8354 (mp0) REVERT: P 371 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8406 (mt-10) REVERT: P 390 GLU cc_start: 0.7970 (pp20) cc_final: 0.7359 (pp20) REVERT: Q 141 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8698 (tmm-80) REVERT: Q 145 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8927 (mp0) REVERT: Q 159 LYS cc_start: 0.9059 (mppt) cc_final: 0.8638 (mppt) REVERT: Q 161 MET cc_start: 0.9325 (mmm) cc_final: 0.8927 (mmm) REVERT: S 276 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8550 (tm-30) REVERT: S 308 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: S 353 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8635 (tp30) REVERT: S 357 ASN cc_start: 0.9213 (m-40) cc_final: 0.8634 (m110) REVERT: S 390 GLU cc_start: 0.8102 (pp20) cc_final: 0.7860 (pp20) REVERT: T 141 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8496 (ttp80) REVERT: T 145 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: T 159 LYS cc_start: 0.8955 (mppt) cc_final: 0.8505 (mppt) REVERT: T 259 ARG cc_start: 0.8961 (ttm110) cc_final: 0.8630 (ttm-80) REVERT: T 263 LYS cc_start: 0.9302 (ttpp) cc_final: 0.8923 (ttpp) REVERT: V 276 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8431 (tm-30) REVERT: V 308 GLU cc_start: 0.8577 (mp0) cc_final: 0.8271 (mp0) REVERT: V 353 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8801 (mm-30) REVERT: V 357 ASN cc_start: 0.9061 (m-40) cc_final: 0.8660 (m110) REVERT: V 374 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8866 (t0) REVERT: V 390 GLU cc_start: 0.8050 (pp20) cc_final: 0.7770 (pp20) REVERT: W 141 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8661 (tmm-80) REVERT: W 145 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9037 (mp0) REVERT: W 159 LYS cc_start: 0.9007 (mppt) cc_final: 0.8625 (mppt) REVERT: W 161 MET cc_start: 0.9344 (mmm) cc_final: 0.8905 (mmm) REVERT: W 263 LYS cc_start: 0.9302 (ttpp) cc_final: 0.8792 (ttpp) REVERT: Y 276 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8569 (tm-30) REVERT: Y 308 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: Y 353 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8989 (mm-30) REVERT: Y 357 ASN cc_start: 0.9059 (m-40) cc_final: 0.8792 (m110) REVERT: Y 371 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: Y 390 GLU cc_start: 0.8309 (pp20) cc_final: 0.7990 (pp20) REVERT: Z 141 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8581 (ttp80) REVERT: Z 145 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: Z 159 LYS cc_start: 0.9064 (mppt) cc_final: 0.8642 (mppt) REVERT: Z 161 MET cc_start: 0.9296 (mmm) cc_final: 0.8740 (mmm) REVERT: b 276 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8517 (tm-30) REVERT: b 308 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: b 371 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8433 (mt-10) REVERT: b 374 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8927 (t0) REVERT: c 137 GLU cc_start: 0.9139 (pp20) cc_final: 0.8736 (pm20) REVERT: c 141 ARG cc_start: 0.8853 (tmm-80) cc_final: 0.8437 (ttp80) REVERT: c 145 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8676 (mp0) REVERT: c 159 LYS cc_start: 0.9003 (mppt) cc_final: 0.8684 (mppt) REVERT: c 161 MET cc_start: 0.9369 (mmm) cc_final: 0.8691 (mmm) REVERT: c 162 MET cc_start: 0.9631 (ptt) cc_final: 0.8816 (ptp) REVERT: c 263 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9038 (ttpp) REVERT: d 32 GLU cc_start: 0.9377 (pt0) cc_final: 0.8817 (pm20) REVERT: e 185 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8658 (mm-30) REVERT: e 276 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8610 (tm-30) REVERT: e 308 GLU cc_start: 0.8419 (mp0) cc_final: 0.8185 (mp0) REVERT: e 353 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8843 (mm-30) REVERT: e 357 ASN cc_start: 0.9139 (m-40) cc_final: 0.8705 (m110) REVERT: e 390 GLU cc_start: 0.8175 (pp20) cc_final: 0.7746 (pp20) REVERT: f 141 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8622 (tmm-80) REVERT: f 145 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8794 (mp0) REVERT: f 159 LYS cc_start: 0.8960 (mppt) cc_final: 0.8584 (mppt) REVERT: f 161 MET cc_start: 0.9341 (mmm) cc_final: 0.8865 (mmm) REVERT: f 240 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8974 (mm-30) REVERT: h 276 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8557 (tm-30) REVERT: h 353 GLU cc_start: 0.9412 (tp30) cc_final: 0.8994 (tp30) REVERT: h 357 ASN cc_start: 0.9106 (m-40) cc_final: 0.8744 (m110) REVERT: h 371 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8634 (mt-10) REVERT: h 374 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8921 (t0) REVERT: i 141 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8508 (ttp80) REVERT: i 145 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: i 159 LYS cc_start: 0.9025 (mppt) cc_final: 0.8666 (mppt) REVERT: i 161 MET cc_start: 0.9334 (mmm) cc_final: 0.8863 (mmm) REVERT: j 32 GLU cc_start: 0.9386 (pt0) cc_final: 0.9172 (pt0) REVERT: k 276 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8570 (tm-30) REVERT: k 308 GLU cc_start: 0.8663 (mp0) cc_final: 0.8250 (mp0) REVERT: k 371 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8436 (mt-10) REVERT: k 390 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: l 141 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8603 (tmm-80) REVERT: l 145 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8918 (mp0) REVERT: l 159 LYS cc_start: 0.9063 (mppt) cc_final: 0.8687 (mppt) REVERT: l 161 MET cc_start: 0.9328 (mmm) cc_final: 0.8930 (mmm) REVERT: n 276 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8569 (tm-30) REVERT: n 308 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: n 353 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8633 (tp30) REVERT: n 357 ASN cc_start: 0.9208 (m-40) cc_final: 0.8633 (m110) REVERT: n 374 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8842 (t0) REVERT: n 390 GLU cc_start: 0.8090 (pp20) cc_final: 0.7651 (pp20) REVERT: o 141 ARG cc_start: 0.8763 (tmm-80) cc_final: 0.8450 (ttp80) REVERT: o 145 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8669 (mp0) REVERT: o 159 LYS cc_start: 0.8960 (mppt) cc_final: 0.8509 (mppt) REVERT: o 263 LYS cc_start: 0.9305 (ttpp) cc_final: 0.8928 (ttpp) outliers start: 72 outliers final: 23 residues processed: 633 average time/residue: 1.0964 time to fit residues: 790.7024 Evaluate side-chains 637 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 584 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 308 GLU Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 188 GLN Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain V residue 374 ASN Chi-restraints excluded: chain W residue 145 GLU Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain Y residue 371 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain b residue 231 CYS Chi-restraints excluded: chain b residue 308 GLU Chi-restraints excluded: chain b residue 374 ASN Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 263 LYS Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain h residue 374 ASN Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain k residue 390 GLU Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain n residue 374 ASN Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 134 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 325 optimal weight: 3.9990 chunk 295 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 ASN M 263 GLN M 360 ASN R 25 GLN ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 ASN h 360 ASN k 357 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.037625 restraints weight = 116323.885| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 3.19 r_work: 0.2403 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39214 Z= 0.142 Angle : 0.630 14.416 53158 Z= 0.322 Chirality : 0.044 0.148 5796 Planarity : 0.004 0.044 7084 Dihedral : 3.925 15.179 5502 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.38 % Allowed : 19.70 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.12), residues: 4942 helix: 2.15 (0.19), residues: 798 sheet: 0.48 (0.17), residues: 938 loop : 0.29 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 141 TYR 0.020 0.001 TYR S 387 PHE 0.021 0.001 PHE Z 195 TRP 0.010 0.001 TRP D 301 HIS 0.001 0.000 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00340 (39200) covalent geometry : angle 0.62980 (53130) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.29091 ( 28) hydrogen bonds : bond 0.03080 ( 1555) hydrogen bonds : angle 5.35041 ( 3993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 633 time to evaluate : 1.593 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: A 276 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 295 GLU cc_start: 0.9188 (pm20) cc_final: 0.8932 (pm20) REVERT: A 308 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: A 353 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8807 (mm-30) REVERT: A 357 ASN cc_start: 0.9054 (m-40) cc_final: 0.8627 (m110) REVERT: A 374 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8834 (t0) REVERT: A 390 GLU cc_start: 0.8001 (pp20) cc_final: 0.7606 (pp20) REVERT: B 136 ARG cc_start: 0.8266 (pmm150) cc_final: 0.7962 (pmm-80) REVERT: B 141 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8659 (tmm-80) REVERT: B 145 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8999 (mp0) REVERT: B 159 LYS cc_start: 0.9005 (mppt) cc_final: 0.8571 (mppt) REVERT: B 161 MET cc_start: 0.9366 (mmm) cc_final: 0.8617 (mmm) REVERT: B 225 LYS cc_start: 0.9291 (mmmt) cc_final: 0.9030 (mmmm) REVERT: B 263 LYS cc_start: 0.9327 (ttpp) cc_final: 0.8935 (ttpp) REVERT: C 24 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8753 (ttpt) REVERT: D 276 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 308 GLU cc_start: 0.8628 (mp0) cc_final: 0.8294 (mp0) REVERT: D 353 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8970 (mm-30) REVERT: D 357 ASN cc_start: 0.9040 (m-40) cc_final: 0.8777 (m110) REVERT: D 371 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8316 (mt-10) REVERT: D 390 GLU cc_start: 0.8254 (pp20) cc_final: 0.8031 (pp20) REVERT: E 141 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8464 (tmm-80) REVERT: E 145 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8828 (mp0) REVERT: E 159 LYS cc_start: 0.8998 (mppt) cc_final: 0.8571 (mppt) REVERT: E 161 MET cc_start: 0.9312 (mmm) cc_final: 0.8775 (mmm) REVERT: F 30 ASN cc_start: 0.8283 (p0) cc_final: 0.7910 (p0) REVERT: G 276 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8517 (tm-30) REVERT: G 308 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: G 371 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8415 (mt-10) REVERT: G 390 GLU cc_start: 0.8810 (pt0) cc_final: 0.8422 (pp20) REVERT: H 159 LYS cc_start: 0.9004 (mppt) cc_final: 0.8629 (mppt) REVERT: H 161 MET cc_start: 0.9412 (mmm) cc_final: 0.8847 (mmm) REVERT: H 162 MET cc_start: 0.9669 (ptt) cc_final: 0.8778 (ptt) REVERT: H 202 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9124 (mt-10) REVERT: H 263 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8993 (ttpp) REVERT: I 30 ASN cc_start: 0.8478 (p0) cc_final: 0.7855 (p0) REVERT: I 32 GLU cc_start: 0.9282 (pt0) cc_final: 0.8909 (pm20) REVERT: J 185 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8663 (mm-30) REVERT: J 276 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8569 (tm-30) REVERT: J 308 GLU cc_start: 0.8459 (mp0) cc_final: 0.8185 (mp0) REVERT: J 353 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8707 (mm-30) REVERT: J 357 ASN cc_start: 0.9109 (m-40) cc_final: 0.8668 (m110) REVERT: J 390 GLU cc_start: 0.8194 (pp20) cc_final: 0.7718 (pp20) REVERT: K 141 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8430 (ttp80) REVERT: K 145 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: K 159 LYS cc_start: 0.8997 (mppt) cc_final: 0.8578 (mppt) REVERT: K 161 MET cc_start: 0.9405 (mmm) cc_final: 0.8807 (mmm) REVERT: K 263 LYS cc_start: 0.9210 (ttpp) cc_final: 0.8789 (ttpp) REVERT: L 24 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.8836 (ttpt) REVERT: M 276 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8574 (tm-30) REVERT: M 353 GLU cc_start: 0.9392 (tp30) cc_final: 0.8996 (tp30) REVERT: M 357 ASN cc_start: 0.9089 (m-40) cc_final: 0.8770 (m110) REVERT: M 371 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8651 (mt-10) REVERT: M 390 GLU cc_start: 0.8188 (pp20) cc_final: 0.7896 (pp20) REVERT: N 137 GLU cc_start: 0.7685 (pm20) cc_final: 0.7475 (pm20) REVERT: N 159 LYS cc_start: 0.9053 (mppt) cc_final: 0.8688 (mppt) REVERT: N 161 MET cc_start: 0.9353 (mmm) cc_final: 0.8873 (mmm) REVERT: O 30 ASN cc_start: 0.8049 (p0) cc_final: 0.6715 (p0) REVERT: O 32 GLU cc_start: 0.9402 (pt0) cc_final: 0.8812 (pm20) REVERT: P 185 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8612 (mm-30) REVERT: P 276 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8590 (tm-30) REVERT: P 308 GLU cc_start: 0.8676 (mp0) cc_final: 0.8248 (mp0) REVERT: P 371 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8470 (mt-10) REVERT: P 390 GLU cc_start: 0.7959 (pp20) cc_final: 0.7324 (pp20) REVERT: Q 141 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8698 (tmm-80) REVERT: Q 145 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8856 (mp0) REVERT: Q 149 GLU cc_start: 0.9054 (pp20) cc_final: 0.8585 (pm20) REVERT: Q 159 LYS cc_start: 0.9051 (mppt) cc_final: 0.8687 (mppt) REVERT: Q 161 MET cc_start: 0.9347 (mmm) cc_final: 0.8945 (mmm) REVERT: S 276 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8558 (tm-30) REVERT: S 308 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: S 353 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8634 (tp30) REVERT: S 357 ASN cc_start: 0.9198 (m-40) cc_final: 0.8606 (m110) REVERT: S 390 GLU cc_start: 0.8153 (pp20) cc_final: 0.7893 (pp20) REVERT: T 141 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8493 (ttp80) REVERT: T 145 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: T 159 LYS cc_start: 0.8968 (mppt) cc_final: 0.8550 (mppt) REVERT: T 202 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9074 (mt-10) REVERT: T 259 ARG cc_start: 0.8939 (ttm110) cc_final: 0.8614 (ttm-80) REVERT: V 276 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8485 (tm-30) REVERT: V 308 GLU cc_start: 0.8565 (mp0) cc_final: 0.8250 (mp0) REVERT: V 353 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8807 (mm-30) REVERT: V 357 ASN cc_start: 0.9047 (m-40) cc_final: 0.8637 (m110) REVERT: V 390 GLU cc_start: 0.8045 (pp20) cc_final: 0.7774 (pp20) REVERT: W 141 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8718 (tmm-80) REVERT: W 145 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: W 159 LYS cc_start: 0.9021 (mppt) cc_final: 0.8567 (mppt) REVERT: W 161 MET cc_start: 0.9365 (mmm) cc_final: 0.8920 (mmm) REVERT: W 225 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9022 (mmmm) REVERT: W 263 LYS cc_start: 0.9335 (ttpp) cc_final: 0.8934 (ttpp) REVERT: Y 276 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8556 (tm-30) REVERT: Y 308 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: Y 353 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8985 (mm-30) REVERT: Y 357 ASN cc_start: 0.9057 (m-40) cc_final: 0.8807 (m110) REVERT: Y 371 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8290 (mt-10) REVERT: Y 390 GLU cc_start: 0.8321 (pp20) cc_final: 0.8028 (pp20) REVERT: Z 145 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: Z 159 LYS cc_start: 0.9008 (mppt) cc_final: 0.8580 (mppt) REVERT: Z 161 MET cc_start: 0.9300 (mmm) cc_final: 0.8764 (mmm) REVERT: a 30 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8230 (p0) REVERT: b 276 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8529 (tm-30) REVERT: b 308 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: b 371 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8439 (mt-10) REVERT: c 137 GLU cc_start: 0.9163 (pp20) cc_final: 0.8792 (pm20) REVERT: c 141 ARG cc_start: 0.8879 (tmm-80) cc_final: 0.8489 (ttp80) REVERT: c 145 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8620 (mp0) REVERT: c 159 LYS cc_start: 0.9001 (mppt) cc_final: 0.8646 (mppt) REVERT: c 161 MET cc_start: 0.9386 (mmm) cc_final: 0.8786 (mmm) REVERT: c 162 MET cc_start: 0.9648 (ptt) cc_final: 0.8651 (ptp) REVERT: c 202 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9147 (mt-10) REVERT: c 263 LYS cc_start: 0.9303 (ttpp) cc_final: 0.9011 (ttpp) REVERT: d 32 GLU cc_start: 0.9378 (pt0) cc_final: 0.8796 (pm20) REVERT: e 185 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8670 (mm-30) REVERT: e 276 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8569 (tm-30) REVERT: e 308 GLU cc_start: 0.8406 (mp0) cc_final: 0.8168 (mp0) REVERT: e 353 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8711 (mm-30) REVERT: e 357 ASN cc_start: 0.9122 (m-40) cc_final: 0.8658 (m110) REVERT: e 390 GLU cc_start: 0.8221 (pp20) cc_final: 0.7728 (pp20) REVERT: f 141 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8595 (ttp80) REVERT: f 145 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: f 159 LYS cc_start: 0.8991 (mppt) cc_final: 0.8628 (mppt) REVERT: f 161 MET cc_start: 0.9377 (mmm) cc_final: 0.8914 (mmm) REVERT: f 240 GLU cc_start: 0.9225 (mm-30) cc_final: 0.9010 (mm-30) REVERT: h 276 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8584 (tm-30) REVERT: h 353 GLU cc_start: 0.9411 (tp30) cc_final: 0.8996 (tp30) REVERT: h 357 ASN cc_start: 0.9108 (m-40) cc_final: 0.8769 (m110) REVERT: h 371 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8640 (mt-10) REVERT: h 374 ASN cc_start: 0.9103 (m-40) cc_final: 0.8900 (t0) REVERT: i 141 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8665 (tmm-80) REVERT: i 145 GLU cc_start: 0.9002 (mp0) cc_final: 0.8689 (mp0) REVERT: i 159 LYS cc_start: 0.9034 (mppt) cc_final: 0.8665 (mppt) REVERT: i 161 MET cc_start: 0.9336 (mmm) cc_final: 0.8900 (mmm) REVERT: j 32 GLU cc_start: 0.9367 (pt0) cc_final: 0.9157 (pt0) REVERT: k 276 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8619 (tm-30) REVERT: k 308 GLU cc_start: 0.8656 (mp0) cc_final: 0.8216 (mp0) REVERT: k 371 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8492 (mt-10) REVERT: k 390 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: l 141 ARG cc_start: 0.9084 (ttp80) cc_final: 0.8658 (tmm-80) REVERT: l 145 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8898 (mp0) REVERT: l 159 LYS cc_start: 0.9051 (mppt) cc_final: 0.8691 (mppt) REVERT: l 161 MET cc_start: 0.9345 (mmm) cc_final: 0.8942 (mmm) REVERT: n 276 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8532 (tm-30) REVERT: n 308 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: n 353 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8640 (tp30) REVERT: n 357 ASN cc_start: 0.9192 (m-40) cc_final: 0.8604 (m110) REVERT: n 374 ASN cc_start: 0.9040 (m-40) cc_final: 0.8839 (t0) REVERT: n 390 GLU cc_start: 0.8105 (pp20) cc_final: 0.7603 (pp20) REVERT: o 141 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8519 (ttp80) REVERT: o 145 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: o 159 LYS cc_start: 0.8958 (mppt) cc_final: 0.8541 (mppt) REVERT: o 227 MET cc_start: 0.9504 (tpp) cc_final: 0.9280 (tpp) outliers start: 56 outliers final: 19 residues processed: 664 average time/residue: 1.1140 time to fit residues: 843.3114 Evaluate side-chains 639 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 598 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 263 LYS Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 308 GLU Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain W residue 145 GLU Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain a residue 30 ASN Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 231 CYS Chi-restraints excluded: chain b residue 308 GLU Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain k residue 390 GLU Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 34 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 452 optimal weight: 10.0000 chunk 431 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 470 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 201 ASN ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN G 188 GLN G 271 GLN G 284 ASN G 374 ASN I 30 ASN J 284 ASN J 374 ASN M 263 GLN M 360 ASN M 374 ASN P 284 ASN P 357 ASN S 284 ASN V 212 GLN V 284 ASN W 201 ASN ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 201 ASN Z 220 HIS b 284 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 284 ASN e 374 ASN h 360 ASN h 374 ASN k 284 ASN k 357 ASN n 284 ASN ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.035818 restraints weight = 117978.930| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 3.17 r_work: 0.2349 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 39214 Z= 0.355 Angle : 0.711 12.636 53158 Z= 0.367 Chirality : 0.045 0.158 5796 Planarity : 0.005 0.098 7084 Dihedral : 4.157 16.994 5502 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.53 % Allowed : 19.80 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.12), residues: 4942 helix: 2.25 (0.19), residues: 798 sheet: 0.49 (0.17), residues: 938 loop : 0.32 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG Z 141 TYR 0.033 0.002 TYR e 387 PHE 0.023 0.001 PHE f 195 TRP 0.008 0.001 TRP A 307 HIS 0.003 0.001 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00815 (39200) covalent geometry : angle 0.71160 (53130) SS BOND : bond 0.00069 ( 14) SS BOND : angle 0.37161 ( 28) hydrogen bonds : bond 0.03844 ( 1555) hydrogen bonds : angle 5.54340 ( 3993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 574 time to evaluate : 1.590 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: A 276 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 308 GLU cc_start: 0.8596 (mp0) cc_final: 0.8331 (mp0) REVERT: A 353 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8848 (mm-30) REVERT: A 357 ASN cc_start: 0.9080 (m-40) cc_final: 0.8674 (m110) REVERT: A 374 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.8821 (t0) REVERT: A 390 GLU cc_start: 0.8025 (pp20) cc_final: 0.7619 (pp20) REVERT: B 141 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8523 (ttp80) REVERT: B 145 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8935 (mp0) REVERT: B 159 LYS cc_start: 0.9051 (mppt) cc_final: 0.8646 (mppt) REVERT: B 161 MET cc_start: 0.9313 (mmm) cc_final: 0.8769 (mmm) REVERT: B 263 LYS cc_start: 0.9311 (ttpp) cc_final: 0.8778 (ttpp) REVERT: D 276 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 308 GLU cc_start: 0.8680 (mp0) cc_final: 0.8361 (mp0) REVERT: D 353 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8981 (mm-30) REVERT: D 357 ASN cc_start: 0.9025 (m-40) cc_final: 0.8744 (m110) REVERT: D 371 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8642 (mt-10) REVERT: D 390 GLU cc_start: 0.8280 (pp20) cc_final: 0.8052 (pp20) REVERT: E 141 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8530 (tmm-80) REVERT: E 145 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8852 (mp0) REVERT: E 159 LYS cc_start: 0.9092 (mppt) cc_final: 0.8621 (mppt) REVERT: E 161 MET cc_start: 0.9278 (mmm) cc_final: 0.8745 (mmm) REVERT: F 30 ASN cc_start: 0.8278 (p0) cc_final: 0.6989 (p0) REVERT: F 32 GLU cc_start: 0.9315 (pt0) cc_final: 0.8800 (pm20) REVERT: G 276 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8565 (tm-30) REVERT: G 308 GLU cc_start: 0.8715 (mp0) cc_final: 0.8293 (mp0) REVERT: G 371 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8363 (mt-10) REVERT: H 141 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8769 (mtm110) REVERT: H 159 LYS cc_start: 0.9052 (mppt) cc_final: 0.8679 (mppt) REVERT: H 161 MET cc_start: 0.9383 (mmm) cc_final: 0.8690 (mmm) REVERT: H 162 MET cc_start: 0.9662 (ptt) cc_final: 0.8914 (ptt) REVERT: H 202 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9159 (mt-10) REVERT: I 30 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7949 (p0) REVERT: I 32 GLU cc_start: 0.9310 (pt0) cc_final: 0.8872 (pm20) REVERT: J 185 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8694 (mm-30) REVERT: J 276 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8630 (tm-30) REVERT: J 308 GLU cc_start: 0.8496 (mp0) cc_final: 0.8230 (mp0) REVERT: J 353 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8869 (mm-30) REVERT: J 357 ASN cc_start: 0.9127 (m-40) cc_final: 0.8699 (m110) REVERT: J 390 GLU cc_start: 0.8237 (pp20) cc_final: 0.7906 (pp20) REVERT: K 141 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8440 (ttp80) REVERT: K 145 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: K 159 LYS cc_start: 0.9059 (mppt) cc_final: 0.8636 (mppt) REVERT: K 161 MET cc_start: 0.9362 (mmm) cc_final: 0.8755 (mmm) REVERT: L 24 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.8848 (ttpt) REVERT: M 276 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8536 (tm-30) REVERT: M 353 GLU cc_start: 0.9438 (tp30) cc_final: 0.9048 (tp30) REVERT: M 357 ASN cc_start: 0.9100 (m-40) cc_final: 0.8779 (m110) REVERT: M 371 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8638 (mt-10) REVERT: M 374 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8867 (t0) REVERT: M 390 GLU cc_start: 0.8235 (pp20) cc_final: 0.7952 (pp20) REVERT: N 141 ARG cc_start: 0.8864 (ptp-110) cc_final: 0.8546 (ptp-110) REVERT: N 159 LYS cc_start: 0.9080 (mppt) cc_final: 0.8688 (mppt) REVERT: N 161 MET cc_start: 0.9330 (mmm) cc_final: 0.8827 (mmm) REVERT: O 32 GLU cc_start: 0.9407 (pt0) cc_final: 0.8692 (pm20) REVERT: P 276 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8585 (tm-30) REVERT: P 308 GLU cc_start: 0.8781 (mp0) cc_final: 0.8371 (mp0) REVERT: P 390 GLU cc_start: 0.8011 (pp20) cc_final: 0.7395 (pp20) REVERT: Q 141 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8684 (tmm-80) REVERT: Q 145 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8955 (mp0) REVERT: Q 159 LYS cc_start: 0.9090 (mppt) cc_final: 0.8698 (mppt) REVERT: Q 161 MET cc_start: 0.9329 (mmm) cc_final: 0.8907 (mmm) REVERT: Q 263 LYS cc_start: 0.9288 (ttpp) cc_final: 0.8798 (ttpp) REVERT: S 276 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8542 (tm-30) REVERT: S 308 GLU cc_start: 0.8615 (mp0) cc_final: 0.8360 (mp0) REVERT: S 353 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8693 (tp30) REVERT: S 357 ASN cc_start: 0.9243 (m-40) cc_final: 0.8673 (m110) REVERT: S 390 GLU cc_start: 0.8189 (pp20) cc_final: 0.7924 (pp20) REVERT: T 141 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8653 (ttp80) REVERT: T 145 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: T 159 LYS cc_start: 0.9034 (mppt) cc_final: 0.8625 (mppt) REVERT: T 259 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8674 (ttm-80) REVERT: V 276 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8492 (tm-30) REVERT: V 308 GLU cc_start: 0.8616 (mp0) cc_final: 0.8322 (mp0) REVERT: V 353 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8845 (mm-30) REVERT: V 357 ASN cc_start: 0.9090 (m-40) cc_final: 0.8678 (m110) REVERT: V 390 GLU cc_start: 0.8060 (pp20) cc_final: 0.7714 (pp20) REVERT: W 141 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8698 (tmm-80) REVERT: W 145 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9053 (mp0) REVERT: W 159 LYS cc_start: 0.9056 (mppt) cc_final: 0.8613 (mppt) REVERT: W 161 MET cc_start: 0.9320 (mmm) cc_final: 0.8787 (mmm) REVERT: W 263 LYS cc_start: 0.9308 (ttpp) cc_final: 0.8755 (ttpp) REVERT: X 24 LYS cc_start: 0.9367 (ttpt) cc_final: 0.8577 (ttpt) REVERT: Y 276 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8564 (tm-30) REVERT: Y 308 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: Y 353 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8964 (mm-30) REVERT: Y 357 ASN cc_start: 0.9045 (m-40) cc_final: 0.8772 (m110) REVERT: Y 371 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8640 (mt-10) REVERT: Y 390 GLU cc_start: 0.8332 (pp20) cc_final: 0.8017 (pp20) REVERT: Z 145 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: Z 159 LYS cc_start: 0.9105 (mppt) cc_final: 0.8684 (mppt) REVERT: Z 161 MET cc_start: 0.9281 (mmm) cc_final: 0.8747 (mmm) REVERT: b 276 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8544 (tm-30) REVERT: b 308 GLU cc_start: 0.8724 (mp0) cc_final: 0.8309 (mp0) REVERT: b 371 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8414 (mt-10) REVERT: b 374 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8990 (t0) REVERT: c 137 GLU cc_start: 0.9210 (pp20) cc_final: 0.8831 (pm20) REVERT: c 141 ARG cc_start: 0.8913 (tmm-80) cc_final: 0.8433 (ttp80) REVERT: c 145 GLU cc_start: 0.8953 (mp0) cc_final: 0.8562 (mp0) REVERT: c 159 LYS cc_start: 0.9022 (mppt) cc_final: 0.8656 (mppt) REVERT: c 161 MET cc_start: 0.9414 (mmm) cc_final: 0.8708 (mmm) REVERT: c 162 MET cc_start: 0.9686 (ptt) cc_final: 0.8896 (ptp) REVERT: d 32 GLU cc_start: 0.9396 (pt0) cc_final: 0.8827 (pm20) REVERT: e 185 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: e 276 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8633 (tm-30) REVERT: e 353 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8876 (mm-30) REVERT: e 357 ASN cc_start: 0.9135 (m-40) cc_final: 0.8704 (m110) REVERT: e 390 GLU cc_start: 0.8268 (pp20) cc_final: 0.7948 (pp20) REVERT: f 141 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8677 (ttp80) REVERT: f 145 GLU cc_start: 0.9052 (mp0) cc_final: 0.8781 (mp0) REVERT: f 159 LYS cc_start: 0.9000 (mppt) cc_final: 0.8589 (mppt) REVERT: f 161 MET cc_start: 0.9339 (mmm) cc_final: 0.8789 (mmm) REVERT: f 240 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8976 (mm-30) REVERT: h 276 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8554 (tm-30) REVERT: h 353 GLU cc_start: 0.9424 (tp30) cc_final: 0.9033 (tp30) REVERT: h 357 ASN cc_start: 0.9153 (m-40) cc_final: 0.8793 (m110) REVERT: h 371 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8602 (mt-10) REVERT: h 374 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8912 (t0) REVERT: i 141 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8559 (ttp80) REVERT: i 145 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8428 (mp0) REVERT: i 159 LYS cc_start: 0.9068 (mppt) cc_final: 0.8676 (mppt) REVERT: i 161 MET cc_start: 0.9327 (mmm) cc_final: 0.8840 (mmm) REVERT: j 32 GLU cc_start: 0.9374 (pt0) cc_final: 0.9133 (pt0) REVERT: k 276 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8571 (tm-30) REVERT: k 308 GLU cc_start: 0.8734 (mp0) cc_final: 0.8319 (mp0) REVERT: k 390 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: l 141 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8629 (tmm-80) REVERT: l 145 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8935 (mp0) REVERT: l 159 LYS cc_start: 0.9086 (mppt) cc_final: 0.8620 (mppt) REVERT: l 161 MET cc_start: 0.9345 (mmm) cc_final: 0.8899 (mmm) REVERT: n 276 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8548 (tm-30) REVERT: n 308 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: n 353 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8675 (tp30) REVERT: n 357 ASN cc_start: 0.9238 (m-40) cc_final: 0.8671 (m110) REVERT: n 390 GLU cc_start: 0.8146 (pp20) cc_final: 0.7891 (pp20) REVERT: o 141 ARG cc_start: 0.8782 (tmm-80) cc_final: 0.8380 (ttp80) REVERT: o 145 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: o 159 LYS cc_start: 0.8988 (mppt) cc_final: 0.8584 (mppt) REVERT: o 227 MET cc_start: 0.9520 (tpp) cc_final: 0.9184 (tpp) REVERT: o 259 ARG cc_start: 0.9093 (ttm-80) cc_final: 0.8612 (ttm-80) outliers start: 62 outliers final: 14 residues processed: 602 average time/residue: 1.1770 time to fit residues: 804.1043 Evaluate side-chains 583 residues out of total 4074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 551 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain M residue 374 ASN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain W residue 145 GLU Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 231 CYS Chi-restraints excluded: chain b residue 374 ASN Chi-restraints excluded: chain e residue 185 GLU Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain h residue 374 ASN Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain k residue 390 GLU Chi-restraints excluded: chain n residue 308 GLU Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 65 optimal weight: 1.9990 chunk 446 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 473 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 373 optimal weight: 0.9980 chunk 439 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN D 374 ASN G 271 GLN ** J 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN M 360 ASN M 374 ASN P 357 ASN R 25 GLN Y 374 ASN a 30 ASN e 374 ASN h 263 GLN h 360 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.037790 restraints weight = 115667.591| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 3.18 r_work: 0.2409 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39214 Z= 0.131 Angle : 0.668 15.034 53158 Z= 0.343 Chirality : 0.044 0.154 5796 Planarity : 0.004 0.053 7084 Dihedral : 3.926 15.963 5502 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.14 % Allowed : 20.29 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.12), residues: 4942 helix: 2.04 (0.19), residues: 798 sheet: 0.49 (0.17), residues: 938 loop : 0.31 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 141 TYR 0.021 0.001 TYR e 387 PHE 0.023 0.001 PHE I 29 TRP 0.011 0.001 TRP b 301 HIS 0.001 0.000 HIS Z 220 Details of bonding type rmsd covalent geometry : bond 0.00314 (39200) covalent geometry : angle 0.66769 (53130) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.37030 ( 28) hydrogen bonds : bond 0.03141 ( 1555) hydrogen bonds : angle 5.43036 ( 3993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16804.17 seconds wall clock time: 286 minutes 32.94 seconds (17192.94 seconds total)