Starting phenix.real_space_refine on Sat Mar 16 18:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/03_2024/8ib2_35329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/03_2024/8ib2_35329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/03_2024/8ib2_35329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/03_2024/8ib2_35329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/03_2024/8ib2_35329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/03_2024/8ib2_35329_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 113 5.16 5 C 9608 2.51 5 N 2568 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ASP 363": "OD1" <-> "OD2" Residue "5 GLU 374": "OE1" <-> "OE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15229 Number of models: 1 Model: "" Number of chains: 11 Chain: "5" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 549 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.04, per 1000 atoms: 0.53 Number of scatterers: 15229 At special positions: 0 Unit cell: (108.23, 93.16, 190.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 10 15.00 O 2930 8.00 N 2568 7.00 C 9608 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: 5.63 Conformation dependent library (CDL) restraints added in 2.9 seconds 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 24 sheets defined 42.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain '5' and resid 345 through 348 No H-bonds generated for 'chain '5' and resid 345 through 348' Processing helix chain '5' and resid 373 through 380 Processing helix chain '5' and resid 384 through 388 Processing helix chain '5' and resid 392 through 401 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.557A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.682A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.524A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 251 through 254 removed outlier: 3.915A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.870A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 346 removed outlier: 5.103A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.837A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 91 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: 3.506A pdb=" N PHE C 124 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 125 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 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: 4.055A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.926A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.698A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 288 through 294 removed outlier: 4.117A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.849A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.410A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 80 through 91 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 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.731A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (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 194 removed outlier: 3.713A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 4.100A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.960A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.691A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.095A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.710A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 355' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.870A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.708A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 113 through 125 removed outlier: 4.037A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.701A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 256' Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 348 removed outlier: 4.090A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 Processing helix chain 'E' and resid 359 through 373 Proline residue: E 367 - end of helix removed outlier: 5.783A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 removed outlier: 3.583A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.862A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 215 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.962A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix removed outlier: 3.643A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.174A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 359 through 373 Proline residue: F 367 - end of helix removed outlier: 5.874A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'B' and resid 297 through 299 removed outlier: 7.477A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= F, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= H, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.566A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= K, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.559A pdb=" N LEU D 104 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'D' and resid 150 through 155 Processing sheet with id= N, first strand: chain 'D' and resid 239 through 241 Processing sheet with id= O, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= P, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= Q, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= R, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 239 through 241 Processing sheet with id= T, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= U, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= V, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= W, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.507A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 239 through 241 543 hydrogen bonds defined for protein. 1365 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: 4.60 Time building geometry restraints manager: 6.10 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: 4945 1.34 - 1.46: 3223 1.46 - 1.58: 7187 1.58 - 1.70: 15 1.70 - 1.82: 196 Bond restraints: 15566 Sorted by residual: bond pdb=" CA VAL F 43 " pdb=" CB VAL F 43 " ideal model delta sigma weight residual 1.531 1.551 -0.020 1.11e-02 8.12e+03 3.32e+00 bond pdb=" CB GLN B 354 " pdb=" CG GLN B 354 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB ASN C 252 " pdb=" CG ASN C 252 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.83e+00 bond pdb=" CA THR E 201 " pdb=" CB THR E 201 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.42e+00 bond pdb=" CG GLN B 354 " pdb=" CD GLN B 354 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.41e+00 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.69: 349 104.69 - 112.51: 7972 112.51 - 120.33: 6441 120.33 - 128.14: 6233 128.14 - 135.96: 110 Bond angle restraints: 21105 Sorted by residual: angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.97 128.58 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CB GLN B 354 " pdb=" CG GLN B 354 " pdb=" CD GLN B 354 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.70e+00 3.46e-01 1.19e+01 angle pdb=" CA GLU E 364 " pdb=" CB GLU E 364 " pdb=" CG GLU E 364 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CB MET 5 365 " pdb=" CG MET 5 365 " pdb=" SD MET 5 365 " ideal model delta sigma weight residual 112.70 103.03 9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N GLU D 83 " pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " ideal model delta sigma weight residual 110.28 115.17 -4.89 1.55e+00 4.16e-01 9.95e+00 ... (remaining 21100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8466 17.94 - 35.89: 768 35.89 - 53.83: 119 53.83 - 71.77: 21 71.77 - 89.72: 12 Dihedral angle restraints: 9386 sinusoidal: 3808 harmonic: 5578 Sorted by residual: dihedral pdb=" CA VAL D 152 " pdb=" C VAL D 152 " pdb=" N MET D 153 " pdb=" CA MET D 153 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLN F 353 " pdb=" C GLN F 353 " pdb=" N GLN F 354 " pdb=" CA GLN F 354 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 9383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1846 0.054 - 0.107: 401 0.107 - 0.161: 86 0.161 - 0.215: 3 0.215 - 0.268: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CB ILE F 250 " pdb=" CA ILE F 250 " pdb=" CG1 ILE F 250 " pdb=" CG2 ILE F 250 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET C 123 " pdb=" N MET C 123 " pdb=" C MET C 123 " pdb=" CB MET C 123 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2335 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP 5 363 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" CG ASP 5 363 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP 5 363 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP 5 363 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO C 112 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO E 243 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.024 5.00e-02 4.00e+02 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2443 2.77 - 3.30: 13614 3.30 - 3.83: 23878 3.83 - 4.37: 28179 4.37 - 4.90: 49833 Nonbonded interactions: 117947 Sorted by model distance: nonbonded pdb=" OG1 THR F 202 " pdb=" OE1 GLU F 205 " model vdw 2.232 2.440 nonbonded pdb=" OG SER F 141 " pdb=" OG SER F 300 " model vdw 2.262 2.440 nonbonded pdb=" OD1 ASP F 157 " pdb=" O3' ADP F 401 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.319 2.440 nonbonded pdb=" NZ LYS C 213 " pdb=" O2' ADP C 401 " model vdw 2.329 2.520 ... (remaining 117942 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 42.560 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15566 Z= 0.203 Angle : 0.688 10.786 21105 Z= 0.354 Chirality : 0.047 0.268 2338 Planarity : 0.005 0.062 2700 Dihedral : 13.903 89.718 5810 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1919 helix: -0.37 (0.18), residues: 750 sheet: 0.74 (0.28), residues: 332 loop : 0.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.003 0.001 HIS E 371 PHE 0.026 0.001 PHE E 124 TYR 0.009 0.001 TYR E 143 ARG 0.009 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: 5 376 PHE cc_start: 0.8161 (t80) cc_final: 0.7868 (t80) REVERT: B 122 ILE cc_start: 0.7942 (mt) cc_final: 0.7682 (mt) REVERT: B 195 GLU cc_start: 0.7678 (tp30) cc_final: 0.7418 (tp30) REVERT: C 72 GLU cc_start: 0.7447 (pp20) cc_final: 0.7214 (pp20) REVERT: C 269 MET cc_start: 0.8282 (mtt) cc_final: 0.7882 (mtp) REVERT: D 117 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7692 (mt-10) REVERT: E 296 ASN cc_start: 0.8844 (m-40) cc_final: 0.8389 (m-40) REVERT: E 313 MET cc_start: 0.8058 (tpp) cc_final: 0.7709 (tpp) REVERT: F 16 MET cc_start: 0.8169 (mmp) cc_final: 0.7950 (mmm) REVERT: F 113 LYS cc_start: 0.7382 (mtmt) cc_final: 0.6828 (pttm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2547 time to fit residues: 75.5427 Evaluate side-chains 152 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15566 Z= 0.171 Angle : 0.533 7.841 21105 Z= 0.255 Chirality : 0.043 0.156 2338 Planarity : 0.004 0.048 2700 Dihedral : 6.244 83.838 2159 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.85 % Allowed : 5.79 % Favored : 93.35 % 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: 0.53 (0.20), residues: 1919 helix: 0.27 (0.20), residues: 738 sheet: 0.58 (0.28), residues: 339 loop : 0.57 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 356 HIS 0.002 0.001 HIS F 275 PHE 0.009 0.001 PHE C 124 TYR 0.011 0.001 TYR C 143 ARG 0.002 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.828 Fit side-chains REVERT: B 117 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7619 (tt0) REVERT: D 132 MET cc_start: 0.8692 (ppp) cc_final: 0.8402 (ppp) REVERT: E 296 ASN cc_start: 0.8840 (m-40) cc_final: 0.8322 (m-40) REVERT: E 313 MET cc_start: 0.8104 (tpp) cc_final: 0.7781 (tpp) REVERT: F 16 MET cc_start: 0.8224 (mmp) cc_final: 0.7954 (mmm) REVERT: F 82 MET cc_start: 0.9038 (tpt) cc_final: 0.8667 (tpt) REVERT: F 113 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7074 (pttm) outliers start: 14 outliers final: 10 residues processed: 163 average time/residue: 0.2310 time to fit residues: 59.6090 Evaluate side-chains 155 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 D 121 GLN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15566 Z= 0.303 Angle : 0.588 7.218 21105 Z= 0.284 Chirality : 0.046 0.162 2338 Planarity : 0.004 0.039 2700 Dihedral : 6.263 89.901 2159 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.40 % Allowed : 8.48 % Favored : 90.12 % 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: 0.53 (0.20), residues: 1919 helix: 0.36 (0.20), residues: 742 sheet: 0.52 (0.28), residues: 339 loop : 0.51 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 340 HIS 0.005 0.001 HIS E 87 PHE 0.009 0.001 PHE B 200 TYR 0.011 0.001 TYR E 143 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.720 Fit side-chains REVERT: 5 396 ASN cc_start: 0.8555 (m-40) cc_final: 0.8297 (m-40) REVERT: B 117 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7828 (tt0) REVERT: B 132 MET cc_start: 0.8827 (ppp) cc_final: 0.8474 (tmm) REVERT: D 123 MET cc_start: 0.9084 (tpp) cc_final: 0.8575 (tpp) REVERT: E 132 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8188 (ttp) REVERT: E 296 ASN cc_start: 0.8820 (m-40) cc_final: 0.8281 (m-40) REVERT: E 313 MET cc_start: 0.8319 (tpp) cc_final: 0.7989 (tpp) REVERT: E 326 LYS cc_start: 0.8697 (tttt) cc_final: 0.8319 (pttp) REVERT: F 16 MET cc_start: 0.8264 (mmp) cc_final: 0.7761 (mmm) REVERT: F 82 MET cc_start: 0.9042 (tpt) cc_final: 0.8781 (tpt) REVERT: F 113 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7143 (pttm) REVERT: F 328 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7838 (mmpt) outliers start: 23 outliers final: 19 residues processed: 170 average time/residue: 0.2314 time to fit residues: 62.0149 Evaluate side-chains 162 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15566 Z= 0.183 Angle : 0.525 6.944 21105 Z= 0.249 Chirality : 0.044 0.134 2338 Planarity : 0.004 0.036 2700 Dihedral : 6.062 88.911 2159 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.10 % Allowed : 10.30 % Favored : 88.60 % 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 (0.20), residues: 1919 helix: 0.55 (0.20), residues: 742 sheet: 0.52 (0.28), residues: 339 loop : 0.56 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.017 0.001 PHE 5 376 TYR 0.007 0.001 TYR E 143 ARG 0.002 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.809 Fit side-chains REVERT: 5 365 MET cc_start: 0.8210 (tpp) cc_final: 0.7810 (tpp) REVERT: 5 396 ASN cc_start: 0.8531 (m-40) cc_final: 0.8245 (m-40) REVERT: B 117 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7823 (tt0) REVERT: B 132 MET cc_start: 0.8905 (ppp) cc_final: 0.8367 (tmm) REVERT: B 163 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7482 (p) REVERT: C 82 MET cc_start: 0.8409 (tpp) cc_final: 0.8168 (tpt) REVERT: D 123 MET cc_start: 0.9089 (tpp) cc_final: 0.8661 (tpp) REVERT: D 227 MET cc_start: 0.8493 (mmm) cc_final: 0.8117 (tpt) REVERT: E 119 MET cc_start: 0.7919 (mtt) cc_final: 0.7712 (mtm) REVERT: E 296 ASN cc_start: 0.8843 (m-40) cc_final: 0.8267 (m-40) REVERT: E 313 MET cc_start: 0.8260 (tpp) cc_final: 0.7967 (tpp) REVERT: E 326 LYS cc_start: 0.8708 (tttt) cc_final: 0.8501 (pttt) REVERT: F 16 MET cc_start: 0.7989 (mmp) cc_final: 0.7478 (mmm) REVERT: F 82 MET cc_start: 0.8990 (tpt) cc_final: 0.8688 (tpt) REVERT: F 113 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7115 (pttt) REVERT: F 201 THR cc_start: 0.9100 (p) cc_final: 0.8830 (t) REVERT: F 328 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7784 (mmpt) outliers start: 18 outliers final: 14 residues processed: 166 average time/residue: 0.2232 time to fit residues: 58.4829 Evaluate side-chains 162 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15566 Z= 0.240 Angle : 0.549 7.016 21105 Z= 0.262 Chirality : 0.045 0.242 2338 Planarity : 0.004 0.034 2700 Dihedral : 6.005 87.002 2159 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.95 % Allowed : 10.79 % Favored : 87.26 % 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 (0.20), residues: 1919 helix: 0.62 (0.20), residues: 745 sheet: 0.51 (0.28), residues: 339 loop : 0.48 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.004 0.001 HIS E 87 PHE 0.010 0.001 PHE 5 376 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.886 Fit side-chains REVERT: 5 396 ASN cc_start: 0.8557 (m-40) cc_final: 0.8254 (m-40) REVERT: B 117 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7838 (tt0) REVERT: B 132 MET cc_start: 0.8875 (ppp) cc_final: 0.8548 (tmm) REVERT: B 163 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7515 (p) REVERT: D 123 MET cc_start: 0.9053 (tpp) cc_final: 0.8637 (tpp) REVERT: D 227 MET cc_start: 0.8556 (mmm) cc_final: 0.8198 (tpt) REVERT: E 296 ASN cc_start: 0.8836 (m-40) cc_final: 0.8270 (m-40) REVERT: F 113 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7163 (pttt) REVERT: F 328 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7825 (mmpt) outliers start: 32 outliers final: 26 residues processed: 174 average time/residue: 0.2304 time to fit residues: 63.6777 Evaluate side-chains 172 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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: 0.8460 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15566 Z= 0.161 Angle : 0.517 8.030 21105 Z= 0.243 Chirality : 0.043 0.184 2338 Planarity : 0.003 0.034 2700 Dihedral : 5.818 85.946 2159 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 11.95 % Favored : 86.40 % 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 (0.20), residues: 1919 helix: 0.76 (0.20), residues: 746 sheet: 0.55 (0.28), residues: 339 loop : 0.56 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.002 0.000 HIS E 87 PHE 0.009 0.001 PHE 5 376 TYR 0.007 0.001 TYR C 143 ARG 0.002 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.782 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8367 (mt) cc_final: 0.8126 (mt) REVERT: 5 396 ASN cc_start: 0.8533 (m-40) cc_final: 0.8235 (m-40) REVERT: B 117 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7813 (tt0) REVERT: B 132 MET cc_start: 0.8873 (ppp) cc_final: 0.8510 (tmm) REVERT: C 78 ASN cc_start: 0.8722 (t0) cc_final: 0.8482 (t0) REVERT: D 123 MET cc_start: 0.9031 (tpp) cc_final: 0.8649 (tpp) REVERT: D 227 MET cc_start: 0.8498 (mmm) cc_final: 0.8160 (tpt) REVERT: E 296 ASN cc_start: 0.8825 (m-40) cc_final: 0.8592 (m-40) REVERT: F 113 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7100 (pttt) REVERT: F 201 THR cc_start: 0.9082 (p) cc_final: 0.8800 (t) REVERT: F 328 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7767 (mmpt) outliers start: 27 outliers final: 22 residues processed: 175 average time/residue: 0.2409 time to fit residues: 66.0091 Evaluate side-chains 174 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15566 Z= 0.169 Angle : 0.526 8.344 21105 Z= 0.246 Chirality : 0.043 0.173 2338 Planarity : 0.003 0.034 2700 Dihedral : 5.712 84.645 2159 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.71 % Allowed : 12.50 % Favored : 85.79 % 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: 0.89 (0.20), residues: 1919 helix: 0.87 (0.20), residues: 742 sheet: 0.55 (0.28), residues: 339 loop : 0.56 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.003 0.000 HIS E 87 PHE 0.008 0.001 PHE B 255 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.655 Fit side-chains REVERT: 5 365 MET cc_start: 0.8375 (tpp) cc_final: 0.7927 (tpp) REVERT: 5 396 ASN cc_start: 0.8531 (m-40) cc_final: 0.8233 (m-40) REVERT: B 117 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7810 (tt0) REVERT: B 132 MET cc_start: 0.8886 (ppp) cc_final: 0.8493 (tmm) REVERT: D 123 MET cc_start: 0.9055 (tpp) cc_final: 0.8679 (tpp) REVERT: D 227 MET cc_start: 0.8506 (mmm) cc_final: 0.8178 (tpt) REVERT: E 296 ASN cc_start: 0.8821 (m-40) cc_final: 0.8581 (m-40) REVERT: F 113 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7122 (pttt) REVERT: F 328 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7523 (mmpt) outliers start: 28 outliers final: 22 residues processed: 174 average time/residue: 0.2260 time to fit residues: 61.4167 Evaluate side-chains 173 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15566 Z= 0.202 Angle : 0.543 9.685 21105 Z= 0.254 Chirality : 0.044 0.160 2338 Planarity : 0.003 0.032 2700 Dihedral : 5.680 83.261 2159 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.83 % Allowed : 12.80 % Favored : 85.37 % 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: 0.88 (0.20), residues: 1919 helix: 0.86 (0.20), residues: 742 sheet: 0.54 (0.28), residues: 339 loop : 0.55 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.009 0.001 PHE B 255 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.760 Fit side-chains REVERT: 5 365 MET cc_start: 0.8290 (tpp) cc_final: 0.7779 (tpp) REVERT: 5 396 ASN cc_start: 0.8547 (m-40) cc_final: 0.8234 (m-40) REVERT: B 117 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7819 (tt0) REVERT: B 132 MET cc_start: 0.8891 (ppp) cc_final: 0.8478 (tmm) REVERT: D 123 MET cc_start: 0.9071 (tpp) cc_final: 0.8701 (tpp) REVERT: D 227 MET cc_start: 0.8505 (mmm) cc_final: 0.8169 (tpt) REVERT: E 296 ASN cc_start: 0.8820 (m-40) cc_final: 0.8586 (m-40) REVERT: F 113 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7125 (pttt) REVERT: F 328 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7435 (mmpt) outliers start: 30 outliers final: 26 residues processed: 174 average time/residue: 0.2325 time to fit residues: 63.1303 Evaluate side-chains 176 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15566 Z= 0.293 Angle : 0.593 9.475 21105 Z= 0.282 Chirality : 0.046 0.154 2338 Planarity : 0.004 0.032 2700 Dihedral : 5.830 81.330 2159 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.71 % Allowed : 13.48 % Favored : 84.82 % 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: 0.82 (0.20), residues: 1919 helix: 0.89 (0.20), residues: 711 sheet: 0.48 (0.28), residues: 339 loop : 0.45 (0.23), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.005 0.001 HIS E 87 PHE 0.010 0.001 PHE B 255 TYR 0.013 0.001 TYR C 143 ARG 0.004 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.744 Fit side-chains REVERT: 5 365 MET cc_start: 0.8298 (tpp) cc_final: 0.7796 (tpp) REVERT: B 117 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7901 (tt0) REVERT: B 132 MET cc_start: 0.8915 (ppp) cc_final: 0.8683 (ppp) REVERT: B 163 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7610 (p) REVERT: D 123 MET cc_start: 0.9095 (tpp) cc_final: 0.8729 (tpp) REVERT: D 227 MET cc_start: 0.8530 (mmm) cc_final: 0.8178 (tpt) REVERT: E 296 ASN cc_start: 0.8837 (m-40) cc_final: 0.8616 (m-40) REVERT: F 113 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7287 (pttt) outliers start: 28 outliers final: 23 residues processed: 165 average time/residue: 0.2360 time to fit residues: 60.4310 Evaluate side-chains 167 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 86 optimal weight: 0.0030 chunk 126 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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: 0.8477 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15566 Z= 0.199 Angle : 0.553 8.532 21105 Z= 0.259 Chirality : 0.044 0.157 2338 Planarity : 0.003 0.031 2700 Dihedral : 5.717 80.397 2159 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.34 % Allowed : 14.09 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.20), residues: 1919 helix: 0.94 (0.20), residues: 718 sheet: 0.50 (0.29), residues: 339 loop : 0.50 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.009 0.001 PHE B 255 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG C 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.738 Fit side-chains REVERT: B 16 MET cc_start: 0.8401 (mtp) cc_final: 0.8052 (mtp) REVERT: B 117 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7859 (tt0) REVERT: B 132 MET cc_start: 0.8899 (ppp) cc_final: 0.8463 (tmm) REVERT: B 163 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7511 (p) REVERT: D 123 MET cc_start: 0.9080 (tpp) cc_final: 0.8726 (tpp) REVERT: D 227 MET cc_start: 0.8491 (mmm) cc_final: 0.8146 (tpt) REVERT: E 296 ASN cc_start: 0.8838 (m-40) cc_final: 0.8610 (m-40) REVERT: F 113 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7143 (pttt) REVERT: F 201 THR cc_start: 0.9106 (p) cc_final: 0.8811 (t) outliers start: 22 outliers final: 20 residues processed: 165 average time/residue: 0.2372 time to fit residues: 61.4241 Evaluate side-chains 169 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.088750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.076147 restraints weight = 26376.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.077698 restraints weight = 17155.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.078970 restraints weight = 11554.858| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15566 Z= 0.161 Angle : 0.542 10.348 21105 Z= 0.251 Chirality : 0.043 0.163 2338 Planarity : 0.003 0.031 2700 Dihedral : 5.548 78.499 2159 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 1.40 % Allowed : 14.09 % Favored : 84.51 % 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: 0.97 (0.20), residues: 1919 helix: 1.04 (0.20), residues: 718 sheet: 0.56 (0.29), residues: 331 loop : 0.52 (0.23), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.002 0.000 HIS E 87 PHE 0.009 0.001 PHE B 255 TYR 0.009 0.001 TYR C 143 ARG 0.002 0.000 ARG 5 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.69 seconds wall clock time: 47 minutes 10.81 seconds (2830.81 seconds total)