Starting phenix.real_space_refine on Fri Mar 15 14:03:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/03_2024/8dmy_27549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/03_2024/8dmy_27549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/03_2024/8dmy_27549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/03_2024/8dmy_27549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/03_2024/8dmy_27549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/03_2024/8dmy_27549_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 7436 2.51 5 N 1986 2.21 5 O 2282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2925 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2925 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.73, per 1000 atoms: 0.57 Number of scatterers: 11796 At special positions: 0 Unit cell: (78.408, 110.484, 169.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 8 15.00 Mg 4 11.99 O 2282 8.00 N 1986 7.00 C 7436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.42 Conformation dependent library (CDL) restraints added in 2.4 seconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 20 sheets defined 39.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.808A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.523A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.943A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.768A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.732A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.586A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.589A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.701A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.640A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.778A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.808A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.523A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.943A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.769A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.732A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.586A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.590A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.701A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.640A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.778A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.807A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.522A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.943A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.768A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.732A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.586A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.591A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.701A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.639A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.778A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.808A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.522A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.943A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.768A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.731A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.587A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.590A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.701A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.641A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 354' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.778A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.417A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 11 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.417A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= K, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.416A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 11 Processing sheet with id= Q, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.417A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 238 through 240 356 hydrogen bonds defined for protein. 912 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: 3.19 Time building geometry restraints manager: 4.73 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: 3660 1.34 - 1.45: 1670 1.45 - 1.57: 6570 1.57 - 1.69: 12 1.69 - 1.81: 140 Bond restraints: 12052 Sorted by residual: bond pdb=" N VAL B 45 " pdb=" CA VAL B 45 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL C 45 " pdb=" CA VAL C 45 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N VAL D 45 " pdb=" CA VAL D 45 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL A 45 " pdb=" CA VAL A 45 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.07e+01 ... (remaining 12047 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.58: 532 107.58 - 114.69: 7117 114.69 - 121.81: 6029 121.81 - 128.92: 2604 128.92 - 136.03: 76 Bond angle restraints: 16358 Sorted by residual: angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" CB VAL A 45 " ideal model delta sigma weight residual 112.36 104.60 7.76 1.85e+00 2.92e-01 1.76e+01 angle pdb=" CA VAL A 45 " pdb=" C VAL A 45 " pdb=" O VAL A 45 " ideal model delta sigma weight residual 121.63 117.98 3.65 9.90e-01 1.02e+00 1.36e+01 angle pdb=" CA VAL D 45 " pdb=" C VAL D 45 " pdb=" O VAL D 45 " ideal model delta sigma weight residual 121.63 117.98 3.65 9.90e-01 1.02e+00 1.36e+01 angle pdb=" CA VAL C 45 " pdb=" C VAL C 45 " pdb=" O VAL C 45 " ideal model delta sigma weight residual 121.63 118.02 3.61 9.90e-01 1.02e+00 1.33e+01 angle pdb=" CA VAL B 45 " pdb=" C VAL B 45 " pdb=" O VAL B 45 " ideal model delta sigma weight residual 121.63 118.06 3.57 9.90e-01 1.02e+00 1.30e+01 ... (remaining 16353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 6943 35.00 - 69.99: 283 69.99 - 104.99: 12 104.99 - 139.98: 4 139.98 - 174.98: 8 Dihedral angle restraints: 7250 sinusoidal: 2932 harmonic: 4318 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.98 -174.98 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.97 -174.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.97 -174.96 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 7247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1595 0.075 - 0.150: 202 0.150 - 0.225: 13 0.225 - 0.300: 1 0.300 - 0.375: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1811 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C PRO D 70 " -0.067 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 71 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 112 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 112 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " -0.028 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 4381 2.88 - 3.39: 9917 3.39 - 3.89: 17592 3.89 - 4.40: 20290 4.40 - 4.90: 36208 Nonbonded interactions: 88388 Sorted by model distance: nonbonded pdb=" O ALA D 174 " pdb=" OG SER D 281 " model vdw 2.379 2.440 nonbonded pdb=" O ALA A 174 " pdb=" OG SER A 281 " model vdw 2.380 2.440 nonbonded pdb=" O ALA B 174 " pdb=" OG SER B 281 " model vdw 2.380 2.440 nonbonded pdb=" O ALA C 174 " pdb=" OG SER C 281 " model vdw 2.381 2.440 nonbonded pdb=" NH1 ARG B 210 " pdb=" OE2 GLU B 214 " model vdw 2.412 2.520 ... (remaining 88383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 375 or resid 401 through 402)) selection = (chain 'B' and (resid 3 through 375 or resid 401 through 402)) selection = chain 'C' selection = chain 'D' } 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: 1.090 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: 0.010 Extract box with map and model: 4.270 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.140 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.004 0.039 12052 Z= 0.237 Angle : 0.622 7.757 16358 Z= 0.353 Chirality : 0.049 0.375 1814 Planarity : 0.004 0.051 2096 Dihedral : 18.681 174.978 4486 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.63 % Allowed : 21.71 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1474 helix: -1.77 (0.20), residues: 528 sheet: 0.76 (0.30), residues: 268 loop : -0.52 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 356 HIS 0.003 0.001 HIS A 101 PHE 0.004 0.001 PHE B 31 TYR 0.006 0.001 TYR D 306 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.354 Fit side-chains REVERT: A 224 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6732 (mp0) REVERT: B 95 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6327 (mtt90) REVERT: B 211 ASP cc_start: 0.8154 (t0) cc_final: 0.7849 (t0) REVERT: B 326 LYS cc_start: 0.8294 (mttp) cc_final: 0.7513 (tttm) REVERT: C 51 ASP cc_start: 0.7386 (p0) cc_final: 0.6942 (t0) REVERT: C 80 ASP cc_start: 0.8122 (m-30) cc_final: 0.7770 (m-30) REVERT: C 95 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6552 (mtm-85) REVERT: C 132 MET cc_start: 0.9013 (ptm) cc_final: 0.8783 (ptm) REVERT: C 211 ASP cc_start: 0.8289 (t0) cc_final: 0.7916 (t0) REVERT: C 326 LYS cc_start: 0.8043 (mttp) cc_final: 0.7675 (mmtt) REVERT: C 372 ARG cc_start: 0.6742 (ttm170) cc_final: 0.6208 (mtm180) REVERT: D 95 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6649 (mtp-110) REVERT: D 358 SER cc_start: 0.8685 (m) cc_final: 0.8414 (t) outliers start: 8 outliers final: 1 residues processed: 206 average time/residue: 0.2502 time to fit residues: 72.6428 Evaluate side-chains 150 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 chunk 134 optimal weight: 0.0070 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS A 121 GLN A 275 HIS B 12 ASN B 101 HIS B 121 GLN B 275 HIS C 12 ASN C 101 HIS C 121 GLN C 275 HIS D 12 ASN D 121 GLN D 275 HIS D 353 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12052 Z= 0.199 Angle : 0.575 5.975 16358 Z= 0.288 Chirality : 0.046 0.147 1814 Planarity : 0.005 0.053 2096 Dihedral : 13.981 179.351 1680 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.25 % Allowed : 20.84 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1474 helix: -0.67 (0.23), residues: 532 sheet: 0.95 (0.31), residues: 260 loop : -0.59 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 356 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE A 255 TYR 0.008 0.001 TYR C 69 ARG 0.004 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 1.405 Fit side-chains REVERT: B 95 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6548 (mtt90) REVERT: B 211 ASP cc_start: 0.7847 (t0) cc_final: 0.7617 (t0) REVERT: B 326 LYS cc_start: 0.8308 (mttp) cc_final: 0.7487 (tttm) REVERT: B 372 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.7263 (mtm180) REVERT: C 51 ASP cc_start: 0.7535 (p0) cc_final: 0.7131 (t0) REVERT: C 80 ASP cc_start: 0.7852 (m-30) cc_final: 0.7540 (m-30) REVERT: C 95 ARG cc_start: 0.7073 (mtm110) cc_final: 0.6819 (mtm-85) REVERT: C 132 MET cc_start: 0.9085 (ptm) cc_final: 0.8881 (ptm) REVERT: C 211 ASP cc_start: 0.7991 (t0) cc_final: 0.7575 (t0) REVERT: C 326 LYS cc_start: 0.8106 (mttp) cc_final: 0.7371 (mmtm) REVERT: D 95 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6770 (mtp-110) REVERT: D 358 SER cc_start: 0.8539 (m) cc_final: 0.8328 (t) outliers start: 41 outliers final: 26 residues processed: 183 average time/residue: 0.2262 time to fit residues: 60.2185 Evaluate side-chains 170 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 0.0070 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 12 ASN C 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12052 Z= 0.302 Angle : 0.612 6.387 16358 Z= 0.303 Chirality : 0.049 0.145 1814 Planarity : 0.005 0.053 2096 Dihedral : 12.780 179.553 1678 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.65 % Allowed : 20.84 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1474 helix: -0.45 (0.23), residues: 548 sheet: 0.60 (0.29), residues: 288 loop : -1.10 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE A 255 TYR 0.011 0.001 TYR C 69 ARG 0.003 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 1.594 Fit side-chains REVERT: A 34 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.7898 (pt) REVERT: A 199 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 65 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7761 (pp) REVERT: B 95 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6775 (mtt90) REVERT: B 326 LYS cc_start: 0.8311 (mttp) cc_final: 0.7485 (tttm) REVERT: B 328 LYS cc_start: 0.8285 (ptpp) cc_final: 0.7989 (ptmm) REVERT: B 372 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7326 (mtm180) REVERT: C 51 ASP cc_start: 0.7773 (p0) cc_final: 0.7274 (t0) REVERT: C 80 ASP cc_start: 0.7870 (m-30) cc_final: 0.7599 (m-30) REVERT: C 93 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: C 211 ASP cc_start: 0.8049 (t0) cc_final: 0.7634 (t0) REVERT: C 326 LYS cc_start: 0.8254 (mttp) cc_final: 0.7491 (mmtm) REVERT: D 95 ARG cc_start: 0.7321 (mtm110) cc_final: 0.7054 (mtm110) REVERT: D 284 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7641 (mttt) REVERT: D 358 SER cc_start: 0.8653 (m) cc_final: 0.8432 (t) outliers start: 46 outliers final: 29 residues processed: 172 average time/residue: 0.2304 time to fit residues: 57.2634 Evaluate side-chains 161 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 135 optimal weight: 6.9990 chunk 143 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12052 Z= 0.237 Angle : 0.569 6.933 16358 Z= 0.278 Chirality : 0.047 0.139 1814 Planarity : 0.005 0.055 2096 Dihedral : 11.588 178.487 1678 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.41 % Allowed : 21.39 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1474 helix: -0.28 (0.24), residues: 546 sheet: 0.20 (0.30), residues: 266 loop : -0.84 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 356 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE A 255 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 1.308 Fit side-chains REVERT: B 95 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6806 (mtt90) REVERT: B 326 LYS cc_start: 0.8287 (mttp) cc_final: 0.7511 (tttm) REVERT: B 328 LYS cc_start: 0.8293 (ptpp) cc_final: 0.7988 (ptmm) REVERT: B 372 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7357 (mtm180) REVERT: C 51 ASP cc_start: 0.7753 (p0) cc_final: 0.7185 (t0) REVERT: C 93 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: C 211 ASP cc_start: 0.7998 (t0) cc_final: 0.7574 (t0) REVERT: C 326 LYS cc_start: 0.8245 (mttp) cc_final: 0.7485 (mmtm) REVERT: D 34 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.7852 (pt) REVERT: D 95 ARG cc_start: 0.7313 (mtm110) cc_final: 0.6938 (mtm180) REVERT: D 334 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: D 358 SER cc_start: 0.8650 (m) cc_final: 0.8448 (t) outliers start: 43 outliers final: 28 residues processed: 172 average time/residue: 0.2295 time to fit residues: 57.1626 Evaluate side-chains 167 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 0.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12052 Z= 0.239 Angle : 0.576 7.409 16358 Z= 0.279 Chirality : 0.047 0.142 1814 Planarity : 0.005 0.054 2096 Dihedral : 10.778 175.331 1678 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.88 % Allowed : 20.60 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1474 helix: -0.19 (0.24), residues: 546 sheet: 0.05 (0.30), residues: 268 loop : -0.86 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.004 0.001 HIS D 161 PHE 0.008 0.001 PHE A 255 TYR 0.009 0.001 TYR C 69 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.254 Fit side-chains REVERT: A 34 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.7927 (pt) REVERT: B 65 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7879 (pp) REVERT: B 95 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6816 (mtt90) REVERT: B 326 LYS cc_start: 0.8291 (mttp) cc_final: 0.7492 (tttm) REVERT: B 328 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7953 (ptmm) REVERT: B 372 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7169 (mtp180) REVERT: C 51 ASP cc_start: 0.7757 (p0) cc_final: 0.7156 (t0) REVERT: C 93 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: C 211 ASP cc_start: 0.8041 (t0) cc_final: 0.7630 (t0) REVERT: C 330 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7325 (mt) REVERT: D 34 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.7869 (pt) REVERT: D 95 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6942 (mtm180) REVERT: D 119 MET cc_start: 0.7487 (mtm) cc_final: 0.7222 (mtm) REVERT: D 334 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: D 358 SER cc_start: 0.8670 (m) cc_final: 0.8145 (p) outliers start: 49 outliers final: 35 residues processed: 176 average time/residue: 0.2344 time to fit residues: 60.1890 Evaluate side-chains 176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12052 Z= 0.359 Angle : 0.646 7.331 16358 Z= 0.317 Chirality : 0.050 0.151 1814 Planarity : 0.005 0.053 2096 Dihedral : 10.326 175.279 1678 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.68 % Allowed : 20.05 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1474 helix: -0.45 (0.23), residues: 544 sheet: -0.10 (0.30), residues: 268 loop : -1.02 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 356 HIS 0.006 0.002 HIS D 161 PHE 0.011 0.001 PHE B 90 TYR 0.010 0.001 TYR C 69 ARG 0.004 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 124 time to evaluate : 1.388 Fit side-chains REVERT: B 65 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7898 (pp) REVERT: B 95 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6804 (mtt90) REVERT: B 326 LYS cc_start: 0.8285 (mttp) cc_final: 0.7603 (tttm) REVERT: B 328 LYS cc_start: 0.8313 (ptpp) cc_final: 0.8001 (ptmm) REVERT: B 372 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7180 (mtp180) REVERT: C 51 ASP cc_start: 0.7795 (p0) cc_final: 0.7188 (t0) REVERT: C 93 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: C 211 ASP cc_start: 0.8135 (t0) cc_final: 0.7737 (t0) REVERT: C 330 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7261 (mt) REVERT: D 95 ARG cc_start: 0.7325 (mtm110) cc_final: 0.7003 (mtm180) REVERT: D 334 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: D 358 SER cc_start: 0.8726 (m) cc_final: 0.8192 (p) outliers start: 59 outliers final: 47 residues processed: 171 average time/residue: 0.2335 time to fit residues: 58.4872 Evaluate side-chains 171 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 120 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.0570 chunk 65 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12052 Z= 0.161 Angle : 0.533 6.018 16358 Z= 0.257 Chirality : 0.045 0.135 1814 Planarity : 0.005 0.056 2096 Dihedral : 8.841 170.912 1678 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.65 % Allowed : 20.92 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1474 helix: -0.04 (0.24), residues: 544 sheet: -0.02 (0.28), residues: 280 loop : -0.88 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 356 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE D 31 TYR 0.006 0.001 TYR A 306 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 1.370 Fit side-chains REVERT: A 80 ASP cc_start: 0.7289 (m-30) cc_final: 0.6950 (m-30) REVERT: B 95 ARG cc_start: 0.7085 (mtm110) cc_final: 0.6806 (mtt90) REVERT: B 326 LYS cc_start: 0.8253 (mttp) cc_final: 0.7665 (tttm) REVERT: B 328 LYS cc_start: 0.8252 (ptpp) cc_final: 0.7948 (ptmm) REVERT: C 51 ASP cc_start: 0.7789 (p0) cc_final: 0.7147 (t0) REVERT: C 93 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: C 211 ASP cc_start: 0.8031 (t0) cc_final: 0.7627 (t0) REVERT: D 95 ARG cc_start: 0.7302 (mtm110) cc_final: 0.6967 (mtm180) REVERT: D 334 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: D 358 SER cc_start: 0.8559 (m) cc_final: 0.7997 (p) outliers start: 46 outliers final: 30 residues processed: 168 average time/residue: 0.2254 time to fit residues: 55.9994 Evaluate side-chains 160 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 112 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12052 Z= 0.357 Angle : 0.632 6.453 16358 Z= 0.309 Chirality : 0.050 0.150 1814 Planarity : 0.005 0.053 2096 Dihedral : 8.523 167.604 1678 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.72 % Allowed : 21.00 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1474 helix: -0.40 (0.23), residues: 558 sheet: -0.10 (0.29), residues: 268 loop : -1.04 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 356 HIS 0.006 0.001 HIS D 161 PHE 0.010 0.001 PHE A 255 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 1.281 Fit side-chains REVERT: B 95 ARG cc_start: 0.7131 (mtm110) cc_final: 0.6824 (mtt90) REVERT: B 326 LYS cc_start: 0.8254 (mttp) cc_final: 0.7714 (tttm) REVERT: B 328 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7968 (ptmm) REVERT: B 372 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7364 (mtm180) REVERT: C 51 ASP cc_start: 0.7851 (p0) cc_final: 0.7186 (t0) REVERT: C 93 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: C 211 ASP cc_start: 0.8051 (t0) cc_final: 0.7649 (t0) REVERT: D 34 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.7844 (pt) REVERT: D 95 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7015 (mtm180) REVERT: D 334 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: D 358 SER cc_start: 0.8710 (m) cc_final: 0.8180 (p) outliers start: 47 outliers final: 38 residues processed: 161 average time/residue: 0.2275 time to fit residues: 53.2685 Evaluate side-chains 166 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12052 Z= 0.143 Angle : 0.532 5.970 16358 Z= 0.254 Chirality : 0.044 0.134 1814 Planarity : 0.005 0.056 2096 Dihedral : 7.363 142.092 1678 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.09 % Allowed : 21.63 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1474 helix: 0.12 (0.25), residues: 534 sheet: 0.08 (0.28), residues: 276 loop : -0.81 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE C 31 TYR 0.006 0.001 TYR A 306 ARG 0.004 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.517 Fit side-chains REVERT: A 34 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.7932 (pt) REVERT: A 80 ASP cc_start: 0.7301 (m-30) cc_final: 0.6956 (m-30) REVERT: A 93 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: B 95 ARG cc_start: 0.7129 (mtm110) cc_final: 0.6811 (mtt90) REVERT: B 326 LYS cc_start: 0.8259 (mttp) cc_final: 0.7717 (tttm) REVERT: B 328 LYS cc_start: 0.8272 (ptpp) cc_final: 0.7984 (ptmm) REVERT: C 51 ASP cc_start: 0.7786 (p0) cc_final: 0.7121 (t0) REVERT: C 211 ASP cc_start: 0.8042 (t0) cc_final: 0.7668 (t0) REVERT: D 95 ARG cc_start: 0.7326 (mtm110) cc_final: 0.7125 (mtm110) REVERT: D 334 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6757 (pm20) REVERT: D 358 SER cc_start: 0.8552 (m) cc_final: 0.8005 (p) outliers start: 39 outliers final: 28 residues processed: 161 average time/residue: 0.2438 time to fit residues: 57.7009 Evaluate side-chains 161 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 117 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12052 Z= 0.332 Angle : 0.629 6.478 16358 Z= 0.305 Chirality : 0.049 0.146 1814 Planarity : 0.005 0.054 2096 Dihedral : 7.377 137.714 1678 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.77 % Allowed : 22.11 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1474 helix: -0.32 (0.23), residues: 558 sheet: 0.01 (0.30), residues: 264 loop : -1.03 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 356 HIS 0.006 0.001 HIS D 161 PHE 0.011 0.001 PHE C 31 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.000 ARG C 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.382 Fit side-chains REVERT: A 128 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7522 (t0) REVERT: B 95 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6831 (mtt90) REVERT: B 326 LYS cc_start: 0.8217 (mttp) cc_final: 0.7679 (tttm) REVERT: B 328 LYS cc_start: 0.8254 (ptpp) cc_final: 0.7960 (ptmm) REVERT: B 372 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.7390 (mtm180) REVERT: C 51 ASP cc_start: 0.7897 (p0) cc_final: 0.7198 (t0) REVERT: C 211 ASP cc_start: 0.8052 (t0) cc_final: 0.7645 (t0) REVERT: D 95 ARG cc_start: 0.7350 (mtm110) cc_final: 0.7006 (mtm180) REVERT: D 334 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: D 358 SER cc_start: 0.8709 (m) cc_final: 0.8196 (p) outliers start: 35 outliers final: 31 residues processed: 155 average time/residue: 0.2376 time to fit residues: 53.3355 Evaluate side-chains 159 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104874 restraints weight = 14958.538| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.86 r_work: 0.3101 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12052 Z= 0.188 Angle : 0.559 6.234 16358 Z= 0.268 Chirality : 0.046 0.138 1814 Planarity : 0.005 0.055 2096 Dihedral : 6.842 115.911 1678 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.93 % Allowed : 21.63 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1474 helix: 0.06 (0.24), residues: 532 sheet: 0.07 (0.28), residues: 276 loop : -0.89 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE C 31 TYR 0.006 0.001 TYR A 143 ARG 0.004 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.01 seconds wall clock time: 45 minutes 58.93 seconds (2758.93 seconds total)