Starting phenix.real_space_refine on Sat Nov 18 00:34:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/11_2023/7sh2_25122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/11_2023/7sh2_25122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/11_2023/7sh2_25122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/11_2023/7sh2_25122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/11_2023/7sh2_25122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/11_2023/7sh2_25122_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 36 5.49 5 Mg 4 5.21 5 S 113 5.16 5 C 13174 2.51 5 N 3597 2.21 5 O 4009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 20933 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3309 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2489 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2692 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2178 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 6 Chain: "G" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 4, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2145 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 5 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 10.80, per 1000 atoms: 0.52 Number of scatterers: 20933 At special positions: 0 Unit cell: (135.792, 125.856, 142.416, 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 113 16.00 P 36 15.00 Mg 4 11.99 O 4009 8.00 N 3597 7.00 C 13174 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: 8.19 Conformation dependent library (CDL) restraints added in 3.6 seconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 18 sheets defined 44.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 116 through 129 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.529A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 386 removed outlier: 5.505A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.526A pdb=" N MET A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 433 removed outlier: 4.677A pdb=" N LYS A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 470 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.229A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 259 removed outlier: 4.234A pdb=" N LYS B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 321 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.508A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 257 through 269 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.813A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.730A pdb=" N MET D 88 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 90 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 91' Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 207 removed outlier: 5.294A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 35 removed outlier: 4.200A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.776A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.831A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 13 through 29 Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.506A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 219 Processing helix chain 'F' and resid 240 through 255 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'G' and resid 18 through 27 removed outlier: 3.813A pdb=" N CYS G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 86 through 95 removed outlier: 4.261A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 160 through 173 removed outlier: 4.298A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 248 removed outlier: 4.164A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 328 Processing helix chain 'H' and resid 11 through 26 removed outlier: 3.997A pdb=" N ASN H 14 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 235 through 242 Processing helix chain 'H' and resid 327 through 338 removed outlier: 3.929A pdb=" N ILE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Proline residue: H 337 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 260 through 262 removed outlier: 7.696A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 148 through 150 removed outlier: 7.785A pdb=" N LEU A 183 " --> pdb=" O THR A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.021A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 162 through 166 removed outlier: 9.291A pdb=" N LEU C 49 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE C 143 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE C 51 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 145 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY C 53 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 147 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 80 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.753A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 190 removed outlier: 3.500A pdb=" N LEU E 39 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 96 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 73 through 78 removed outlier: 4.085A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 42 through 44 removed outlier: 4.047A pdb=" N THR F 43 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.573A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 203 " --> pdb=" O PHE F 160 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 263 through 266 Processing sheet with id= K, first strand: chain 'F' and resid 442 through 445 removed outlier: 3.522A pdb=" N ASP F 445 " --> pdb=" O GLY F 462 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 11 through 15 Processing sheet with id= M, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.585A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.885A pdb=" N ASN G 52 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET G 259 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.113A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 205 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.648A pdb=" N THR H 6 " --> pdb=" O ILE H 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 118 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 91 through 97 removed outlier: 3.523A pdb=" N GLU H 375 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 363 " --> pdb=" O ILE H 349 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 322 through 324 removed outlier: 4.659A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 254 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE H 324 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL H 252 " --> pdb=" O PHE H 324 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 255 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET H 284 " --> pdb=" O ALA H 265 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2454 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: 5.95 Time building geometry restraints manager: 8.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6866 1.36 - 1.51: 5506 1.51 - 1.66: 8790 1.66 - 1.80: 100 1.80 - 1.95: 70 Bond restraints: 21332 Sorted by residual: bond pdb=" N MET F 224 " pdb=" CA MET F 224 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.42e+00 bond pdb=" CG1 ILE G 324 " pdb=" CD1 ILE G 324 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.36e+00 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C THR G 29 " pdb=" N PRO G 30 " ideal model delta sigma weight residual 1.335 1.349 -0.015 1.28e-02 6.10e+03 1.32e+00 bond pdb=" CA ASN F 286 " pdb=" CB ASN F 286 " ideal model delta sigma weight residual 1.535 1.557 -0.021 1.90e-02 2.77e+03 1.27e+00 ... (remaining 21327 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.96: 657 106.96 - 114.26: 12826 114.26 - 121.55: 10546 121.55 - 128.84: 4752 128.84 - 136.14: 138 Bond angle restraints: 28919 Sorted by residual: angle pdb=" C SER E 79 " pdb=" CA SER E 79 " pdb=" CB SER E 79 " ideal model delta sigma weight residual 116.54 110.32 6.22 1.15e+00 7.56e-01 2.93e+01 angle pdb=" CA PRO F 48 " pdb=" N PRO F 48 " pdb=" CD PRO F 48 " ideal model delta sigma weight residual 112.00 105.04 6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" C ILE G 324 " pdb=" N GLU G 325 " pdb=" CA GLU G 325 " ideal model delta sigma weight residual 120.29 114.08 6.21 1.42e+00 4.96e-01 1.92e+01 angle pdb=" N GLU G 325 " pdb=" CA GLU G 325 " pdb=" CB GLU G 325 " ideal model delta sigma weight residual 110.16 116.34 -6.18 1.48e+00 4.57e-01 1.74e+01 angle pdb=" N VAL G 16 " pdb=" CA VAL G 16 " pdb=" C VAL G 16 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 ... (remaining 28914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 12611 35.05 - 70.11: 300 70.11 - 105.16: 21 105.16 - 140.22: 2 140.22 - 175.27: 1 Dihedral angle restraints: 12935 sinusoidal: 5473 harmonic: 7462 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 177.99 122.01 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 57.22 -124.95 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " pdb=" P DG T 23 " ideal model delta sinusoidal sigma weight residual -140.00 35.27 -175.27 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2543 0.043 - 0.085: 593 0.085 - 0.128: 193 0.128 - 0.170: 11 0.170 - 0.213: 6 Chirality restraints: 3346 Sorted by residual: chirality pdb=" CB ILE G 103 " pdb=" CA ILE G 103 " pdb=" CG1 ILE G 103 " pdb=" CG2 ILE G 103 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE G 251 " pdb=" CA ILE G 251 " pdb=" CG1 ILE G 251 " pdb=" CG2 ILE G 251 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA THR F 47 " pdb=" N THR F 47 " pdb=" C THR F 47 " pdb=" CB THR F 47 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 3343 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " -0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO F 48 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 167 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 168 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 488 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 489 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.025 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 395 2.69 - 3.24: 19941 3.24 - 3.79: 33232 3.79 - 4.35: 42987 4.35 - 4.90: 71254 Nonbonded interactions: 167809 Sorted by model distance: nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.135 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.144 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.169 2.170 nonbonded pdb=" O LEU G 326 " pdb=" OG1 THR G 330 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR F 92 " pdb=" OG1 THR F 218 " model vdw 2.202 2.440 ... (remaining 167804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.610 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: 0.020 Extract box with map and model: 14.270 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 53.210 Find NCS groups from input model: 0.750 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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 : 0.002 0.060 21332 Z= 0.143 Angle : 0.560 9.916 28919 Z= 0.292 Chirality : 0.041 0.213 3346 Planarity : 0.004 0.124 3560 Dihedral : 15.060 175.269 8067 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.43 % 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 (0.17), residues: 2497 helix: 1.46 (0.15), residues: 1225 sheet: 0.27 (0.27), residues: 440 loop : -1.43 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 2.430 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2899 time to fit residues: 136.3873 Evaluate side-chains 207 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 5.9990 chunk 191 optimal weight: 0.0040 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 229 optimal weight: 20.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN D 124 HIS D 236 GLN D 305 HIS D 313 ASN E 93 HIS F 463 GLN G 9 ASN G 54 HIS G 190 ASN H 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21332 Z= 0.153 Angle : 0.501 8.351 28919 Z= 0.255 Chirality : 0.040 0.153 3346 Planarity : 0.003 0.045 3560 Dihedral : 11.017 175.936 2992 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.96 % Allowed : 7.66 % Favored : 91.38 % 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: 0.64 (0.18), residues: 2497 helix: 1.64 (0.15), residues: 1226 sheet: 0.19 (0.26), residues: 448 loop : -1.31 (0.22), residues: 823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 2.283 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 260 average time/residue: 0.3114 time to fit residues: 128.9595 Evaluate side-chains 234 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1882 time to fit residues: 8.9244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 0.0670 chunk 156 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 204 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 196 ASN E 164 ASN F 67 GLN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS G 190 ASN H 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21332 Z= 0.291 Angle : 0.619 9.069 28919 Z= 0.317 Chirality : 0.044 0.234 3346 Planarity : 0.005 0.063 3560 Dihedral : 11.398 177.374 2992 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.48 % Allowed : 12.10 % Favored : 86.42 % 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: 0.03 (0.17), residues: 2497 helix: 1.02 (0.15), residues: 1224 sheet: 0.11 (0.26), residues: 430 loop : -1.48 (0.21), residues: 843 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 272 average time/residue: 0.3552 time to fit residues: 149.6382 Evaluate side-chains 227 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2193 time to fit residues: 9.3554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 154 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 236 GLN E 164 ASN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 HIS H 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21332 Z= 0.179 Angle : 0.523 7.636 28919 Z= 0.267 Chirality : 0.040 0.163 3346 Planarity : 0.003 0.048 3560 Dihedral : 11.214 176.281 2992 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.04 % Allowed : 14.36 % Favored : 84.60 % 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: 0.22 (0.17), residues: 2497 helix: 1.26 (0.15), residues: 1224 sheet: 0.03 (0.26), residues: 429 loop : -1.43 (0.21), residues: 844 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 252 average time/residue: 0.3362 time to fit residues: 133.5771 Evaluate side-chains 219 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1958 time to fit residues: 6.9593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 182 optimal weight: 0.0040 chunk 100 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 164 ASN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS H 37 ASN H 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21332 Z= 0.203 Angle : 0.528 10.882 28919 Z= 0.267 Chirality : 0.040 0.161 3346 Planarity : 0.003 0.047 3560 Dihedral : 11.198 176.614 2992 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.17 % Allowed : 15.71 % Favored : 83.12 % 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: 0.18 (0.17), residues: 2497 helix: 1.20 (0.15), residues: 1230 sheet: 0.02 (0.26), residues: 436 loop : -1.43 (0.21), residues: 831 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 226 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 246 average time/residue: 0.3365 time to fit residues: 130.2456 Evaluate side-chains 229 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1847 time to fit residues: 9.1306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 164 ASN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21332 Z= 0.249 Angle : 0.564 11.231 28919 Z= 0.286 Chirality : 0.042 0.172 3346 Planarity : 0.004 0.047 3560 Dihedral : 11.259 177.127 2992 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.39 % Allowed : 16.23 % Favored : 82.38 % 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: 0.02 (0.17), residues: 2497 helix: 1.01 (0.15), residues: 1233 sheet: -0.10 (0.25), residues: 449 loop : -1.40 (0.22), residues: 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 245 average time/residue: 0.3282 time to fit residues: 125.1167 Evaluate side-chains 222 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1886 time to fit residues: 9.2458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 178 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 243 optimal weight: 20.0000 chunk 152 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 164 ASN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS G 79 HIS H 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21332 Z= 0.178 Angle : 0.533 13.515 28919 Z= 0.269 Chirality : 0.041 0.385 3346 Planarity : 0.003 0.047 3560 Dihedral : 11.162 176.605 2992 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.74 % Allowed : 17.15 % Favored : 82.11 % 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: 0.11 (0.17), residues: 2497 helix: 1.13 (0.15), residues: 1233 sheet: -0.11 (0.25), residues: 448 loop : -1.39 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 237 average time/residue: 0.3424 time to fit residues: 125.7563 Evaluate side-chains 215 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2013 time to fit residues: 6.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 191 optimal weight: 0.2980 chunk 221 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 236 GLN E 164 ASN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21332 Z= 0.178 Angle : 0.544 13.539 28919 Z= 0.273 Chirality : 0.041 0.384 3346 Planarity : 0.003 0.047 3560 Dihedral : 11.122 176.563 2992 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.44 % Allowed : 17.97 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.17), residues: 2497 helix: 1.14 (0.15), residues: 1233 sheet: -0.10 (0.25), residues: 450 loop : -1.37 (0.22), residues: 814 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 220 average time/residue: 0.3443 time to fit residues: 118.4136 Evaluate side-chains 203 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1955 time to fit residues: 4.8604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 136 optimal weight: 0.0570 chunk 98 optimal weight: 0.4980 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 41 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 236 GLN E 164 ASN F 226 ASN G 54 HIS H 37 ASN H 245 ASN H 247 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21332 Z= 0.166 Angle : 0.534 14.329 28919 Z= 0.269 Chirality : 0.040 0.383 3346 Planarity : 0.003 0.047 3560 Dihedral : 11.074 176.450 2992 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.52 % Allowed : 17.49 % Favored : 81.98 % 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: 0.22 (0.17), residues: 2497 helix: 1.22 (0.15), residues: 1229 sheet: -0.01 (0.26), residues: 447 loop : -1.37 (0.22), residues: 821 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 221 average time/residue: 0.3542 time to fit residues: 121.8673 Evaluate side-chains 204 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 2.378 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2138 time to fit residues: 5.3067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 4.9990 chunk 146 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 155 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS H 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21332 Z= 0.163 Angle : 0.541 14.250 28919 Z= 0.271 Chirality : 0.040 0.377 3346 Planarity : 0.003 0.047 3560 Dihedral : 11.064 176.416 2992 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.26 % Allowed : 18.06 % Favored : 81.68 % 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: 0.24 (0.17), residues: 2497 helix: 1.23 (0.15), residues: 1229 sheet: 0.02 (0.26), residues: 446 loop : -1.37 (0.22), residues: 822 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 216 average time/residue: 0.3658 time to fit residues: 123.1818 Evaluate side-chains 202 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2021 time to fit residues: 4.9165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 201 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN C 213 GLN D 124 HIS D 236 GLN G 54 HIS H 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.184200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148106 restraints weight = 28888.739| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.36 r_work: 0.3820 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21332 Z= 0.148 Angle : 0.529 13.946 28919 Z= 0.266 Chirality : 0.040 0.368 3346 Planarity : 0.004 0.086 3560 Dihedral : 11.006 176.182 2992 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.13 % Allowed : 18.23 % Favored : 81.64 % 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: 0.33 (0.18), residues: 2497 helix: 1.35 (0.15), residues: 1224 sheet: 0.05 (0.26), residues: 445 loop : -1.37 (0.22), residues: 828 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4403.68 seconds wall clock time: 82 minutes 18.04 seconds (4938.04 seconds total)