Starting phenix.real_space_refine on Sat Dec 9 17:55:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/12_2023/8dmy_27549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/12_2023/8dmy_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_27549/12_2023/8dmy_27549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/12_2023/8dmy_27549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/12_2023/8dmy_27549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/12_2023/8dmy_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-1.21rc1-5172/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: 6.57, per 1000 atoms: 0.56 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: 4.41 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: 2.43 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: 3.21 Time building geometry restraints manager: 4.77 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: 0.970 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: 4.100 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.740 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- 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 : 1.242 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 206 average time/residue: 0.2539 time to fit residues: 73.4190 Evaluate side-chains 147 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1047 time to fit residues: 1.9993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 86 optimal weight: 0.2980 chunk 134 optimal weight: 0.0070 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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: 0.8034 moved from start: 0.1474 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= 0.161 Angle : 0.563 6.024 16358 Z= 0.281 Chirality : 0.045 0.143 1814 Planarity : 0.005 0.053 2096 Dihedral : 13.981 178.726 1678 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.17 % Allowed : 21.00 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1474 helix: -0.60 (0.23), residues: 532 sheet: 0.97 (0.31), residues: 260 loop : -0.57 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 356 HIS 0.004 0.001 HIS D 161 PHE 0.005 0.001 PHE C 31 TYR 0.009 0.001 TYR A 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 193 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 1.248 Fit side-chains outliers start: 40 outliers final: 26 residues processed: 182 average time/residue: 0.2207 time to fit residues: 58.6620 Evaluate side-chains 167 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1067 time to fit residues: 6.7804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 0.0070 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.0142 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12052 Z= 0.344 Angle : 0.639 6.707 16358 Z= 0.319 Chirality : 0.051 0.154 1814 Planarity : 0.005 0.053 2096 Dihedral : 12.940 178.087 1678 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.58 % Allowed : 21.63 % Favored : 76.78 % 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: -0.91 (0.21), residues: 1474 helix: -0.55 (0.23), residues: 548 sheet: 0.62 (0.30), residues: 288 loop : -1.14 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 79 HIS 0.005 0.001 HIS D 161 PHE 0.011 0.001 PHE A 255 TYR 0.012 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 157 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.360 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 152 average time/residue: 0.2570 time to fit residues: 56.8540 Evaluate side-chains 138 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1381 time to fit residues: 4.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12052 Z= 0.332 Angle : 0.627 7.087 16358 Z= 0.310 Chirality : 0.050 0.150 1814 Planarity : 0.005 0.054 2096 Dihedral : 11.744 176.196 1678 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.54 % Allowed : 21.24 % Favored : 76.23 % 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: -1.03 (0.21), residues: 1474 helix: -0.54 (0.23), residues: 544 sheet: 0.04 (0.30), residues: 268 loop : -1.00 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE C 31 TYR 0.011 0.001 TYR C 69 ARG 0.003 0.001 ARG A 254 *********************** 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 162 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.300 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 153 average time/residue: 0.2301 time to fit residues: 51.5497 Evaluate side-chains 141 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1074 time to fit residues: 5.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12052 Z= 0.270 Angle : 0.596 7.325 16358 Z= 0.290 Chirality : 0.048 0.143 1814 Planarity : 0.005 0.054 2096 Dihedral : 10.971 173.722 1678 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.90 % Allowed : 21.00 % Favored : 77.10 % 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: -0.94 (0.22), residues: 1474 helix: -0.32 (0.24), residues: 540 sheet: -0.06 (0.29), residues: 268 loop : -1.01 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 356 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE C 31 TYR 0.008 0.001 TYR C 69 ARG 0.002 0.000 ARG C 210 *********************** 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 145 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.470 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 138 average time/residue: 0.2325 time to fit residues: 47.1107 Evaluate side-chains 133 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1174 time to fit residues: 5.1367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.8173 moved from start: 0.2674 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= 0.355 Angle : 0.648 7.648 16358 Z= 0.318 Chirality : 0.050 0.151 1814 Planarity : 0.005 0.054 2096 Dihedral : 10.588 179.730 1678 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.35 % Allowed : 21.79 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.21), residues: 1474 helix: -0.48 (0.23), residues: 540 sheet: -0.14 (0.28), residues: 276 loop : -1.18 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 356 HIS 0.006 0.001 HIS D 161 PHE 0.011 0.001 PHE B 90 TYR 0.010 0.001 TYR C 143 ARG 0.004 0.000 ARG D 254 *********************** 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 136 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.385 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 128 average time/residue: 0.2352 time to fit residues: 44.3275 Evaluate side-chains 124 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1098 time to fit residues: 3.9052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12052 Z= 0.295 Angle : 0.607 6.679 16358 Z= 0.296 Chirality : 0.048 0.144 1814 Planarity : 0.005 0.054 2096 Dihedral : 9.489 177.325 1678 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 21.32 % 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: -1.09 (0.21), residues: 1474 helix: -0.42 (0.24), residues: 542 sheet: -0.14 (0.29), residues: 264 loop : -1.13 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE A 255 TYR 0.008 0.001 TYR A 143 ARG 0.003 0.000 ARG D 290 *********************** 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 132 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.368 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 128 average time/residue: 0.2389 time to fit residues: 45.2052 Evaluate side-chains 124 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1175 time to fit residues: 2.9748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.0060 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.0170 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.3636 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12052 Z= 0.191 Angle : 0.556 5.998 16358 Z= 0.268 Chirality : 0.045 0.137 1814 Planarity : 0.005 0.055 2096 Dihedral : 8.060 158.318 1678 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 21.16 % Favored : 77.81 % 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: -0.77 (0.22), residues: 1474 helix: -0.02 (0.25), residues: 528 sheet: -0.09 (0.28), residues: 274 loop : -1.01 (0.23), residues: 672 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 0.008 0.001 PHE D 31 TYR 0.007 0.001 TYR A 143 ARG 0.002 0.000 ARG C 210 *********************** 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 138 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.357 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 131 average time/residue: 0.2481 time to fit residues: 47.4485 Evaluate side-chains 128 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1100 time to fit residues: 3.2746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 125 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12052 Z= 0.134 Angle : 0.529 6.132 16358 Z= 0.250 Chirality : 0.044 0.133 1814 Planarity : 0.004 0.056 2096 Dihedral : 6.861 123.073 1678 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.55 % Allowed : 21.55 % Favored : 77.89 % 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: -0.45 (0.22), residues: 1474 helix: 0.26 (0.25), residues: 530 sheet: 0.12 (0.28), residues: 272 loop : -0.85 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.003 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 137 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.367 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 134 average time/residue: 0.2317 time to fit residues: 45.7391 Evaluate side-chains 128 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1078 time to fit residues: 2.0880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12052 Z= 0.307 Angle : 0.625 6.452 16358 Z= 0.302 Chirality : 0.048 0.145 1814 Planarity : 0.005 0.054 2096 Dihedral : 6.984 117.701 1678 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.32 % Allowed : 22.11 % Favored : 77.58 % 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: -0.85 (0.22), residues: 1474 helix: -0.15 (0.24), residues: 540 sheet: -0.11 (0.29), residues: 252 loop : -0.99 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 356 HIS 0.006 0.001 HIS D 161 PHE 0.009 0.001 PHE A 255 TYR 0.009 0.001 TYR A 143 ARG 0.002 0.000 ARG D 254 ********************** 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 126 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.389 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.2812 time to fit residues: 52.2355 Evaluate side-chains 126 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2488 time to fit residues: 4.8524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 49 optimal weight: 0.0010 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.123763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104195 restraints weight = 14998.820| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.89 r_work: 0.3085 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12052 Z= 0.225 Angle : 0.583 6.506 16358 Z= 0.279 Chirality : 0.046 0.139 1814 Planarity : 0.005 0.054 2096 Dihedral : 6.719 103.824 1678 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.40 % Allowed : 21.71 % Favored : 77.89 % 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: -0.69 (0.22), residues: 1474 helix: 0.03 (0.24), residues: 528 sheet: -0.10 (0.29), residues: 252 loop : -0.90 (0.23), residues: 694 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 C 31 TYR 0.007 0.001 TYR A 143 ARG 0.003 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.54 seconds wall clock time: 45 minutes 25.16 seconds (2725.16 seconds total)