Starting phenix.real_space_refine on Mon Mar 18 12:48:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/03_2024/7sh2_25122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/03_2024/7sh2_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_25122/03_2024/7sh2_25122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/03_2024/7sh2_25122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/03_2024/7sh2_25122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sh2_25122/03_2024/7sh2_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.59, per 1000 atoms: 0.55 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: 8.45 Conformation dependent library (CDL) restraints added in 3.7 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: 3.97 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: 6.12 Time building geometry restraints manager: 9.16 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: 12648 35.05 - 70.11: 327 70.11 - 105.16: 21 105.16 - 140.22: 2 140.22 - 175.27: 1 Dihedral angle restraints: 12999 sinusoidal: 5537 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 12996 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: 4.120 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: 15.480 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 55.430 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.330 ------------------------------------------------------------------------------- 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 : 15.294 175.269 8131 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 259 HIS 0.004 0.001 HIS F 74 PHE 0.023 0.001 PHE F 205 TYR 0.015 0.001 TYR E 324 ARG 0.006 0.000 ARG F 36 *********************** 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 : 2.355 Fit side-chains REVERT: A 168 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7812 (tp30) REVERT: A 307 GLU cc_start: 0.7134 (tp30) cc_final: 0.6828 (tp30) REVERT: C 245 LYS cc_start: 0.7448 (tptt) cc_final: 0.6955 (mtmm) REVERT: D 80 LYS cc_start: 0.7291 (tppt) cc_final: 0.6384 (tmtt) REVERT: F 14 ASP cc_start: 0.6320 (m-30) cc_final: 0.5925 (m-30) REVERT: H 148 TYR cc_start: 0.5798 (m-80) cc_final: 0.5592 (m-80) REVERT: H 371 LEU cc_start: 0.5549 (mt) cc_final: 0.5318 (mt) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.2840 time to fit residues: 133.2640 Evaluate side-chains 212 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.6682 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21332 Z= 0.150 Angle : 0.496 8.351 28919 Z= 0.252 Chirality : 0.040 0.155 3346 Planarity : 0.003 0.045 3560 Dihedral : 11.747 175.164 3056 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.96 % Allowed : 7.40 % Favored : 91.64 % 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: 0.63 (0.18), residues: 2497 helix: 1.64 (0.15), residues: 1226 sheet: 0.20 (0.26), residues: 448 loop : -1.32 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 259 HIS 0.005 0.001 HIS G 54 PHE 0.014 0.001 PHE E 328 TYR 0.019 0.001 TYR F 233 ARG 0.003 0.000 ARG F 20 *********************** 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 : 2.210 Fit side-chains REVERT: A 168 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7788 (tp30) REVERT: A 307 GLU cc_start: 0.7189 (tp30) cc_final: 0.6850 (tp30) REVERT: B 45 MET cc_start: 0.7778 (mtp) cc_final: 0.7529 (mtm) REVERT: D 80 LYS cc_start: 0.7399 (tppt) cc_final: 0.6496 (tmtt) REVERT: F 14 ASP cc_start: 0.6449 (m-30) cc_final: 0.6070 (m-30) REVERT: H 44 MET cc_start: 0.5619 (tpt) cc_final: 0.4576 (tpt) REVERT: H 148 TYR cc_start: 0.6063 (m-80) cc_final: 0.5565 (m-80) outliers start: 22 outliers final: 16 residues processed: 260 average time/residue: 0.3015 time to fit residues: 124.7073 Evaluate side-chains 232 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 205 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 248 optimal weight: 30.0000 chunk 204 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 64 HIS C 213 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 196 ASN D 236 GLN E 93 HIS E 164 ASN F 67 GLN F 226 ASN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21332 Z= 0.341 Angle : 0.643 9.464 28919 Z= 0.328 Chirality : 0.045 0.206 3346 Planarity : 0.005 0.063 3560 Dihedral : 11.935 176.830 3056 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.87 % Allowed : 11.71 % 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: -0.05 (0.17), residues: 2497 helix: 0.93 (0.15), residues: 1224 sheet: 0.09 (0.26), residues: 434 loop : -1.48 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 290 HIS 0.022 0.002 HIS E 93 PHE 0.023 0.002 PHE E 328 TYR 0.025 0.002 TYR B 71 ARG 0.007 0.001 ARG D 175 *********************** 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: 43 poor density : 241 time to evaluate : 2.412 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7758 (tp30) REVERT: A 287 MET cc_start: 0.7637 (tmm) cc_final: 0.7401 (tmm) REVERT: A 307 GLU cc_start: 0.7297 (tp30) cc_final: 0.6901 (tp30) REVERT: C 91 ASP cc_start: 0.6528 (m-30) cc_final: 0.6287 (m-30) REVERT: C 97 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6705 (mp) REVERT: C 197 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6793 (tp) REVERT: C 288 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.4912 (m-80) REVERT: C 316 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.6186 (t70) REVERT: F 23 ILE cc_start: 0.6913 (mm) cc_final: 0.6492 (mm) REVERT: F 296 TRP cc_start: 0.5939 (t60) cc_final: 0.5586 (t60) REVERT: F 415 TRP cc_start: 0.5864 (OUTLIER) cc_final: 0.5404 (p-90) REVERT: F 468 ILE cc_start: 0.8337 (mm) cc_final: 0.7833 (mm) REVERT: G 153 SER cc_start: 0.8230 (t) cc_final: 0.7931 (m) REVERT: G 262 HIS cc_start: 0.7012 (m170) cc_final: 0.6593 (m170) REVERT: G 307 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: H 148 TYR cc_start: 0.6233 (m-80) cc_final: 0.5726 (m-80) outliers start: 43 outliers final: 24 residues processed: 270 average time/residue: 0.3302 time to fit residues: 137.5476 Evaluate side-chains 239 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 415 TRP Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU 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: 2.9990 chunk 109 optimal weight: 0.0770 chunk 154 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 E 93 HIS E 164 ASN G 54 HIS H 37 ASN ** H 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2529 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= 0.196 Angle : 0.527 8.017 28919 Z= 0.269 Chirality : 0.040 0.163 3346 Planarity : 0.003 0.048 3560 Dihedral : 11.759 175.665 3056 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.65 % Allowed : 13.88 % Favored : 84.46 % 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: 0.15 (0.17), residues: 2497 helix: 1.18 (0.15), residues: 1224 sheet: 0.03 (0.26), residues: 431 loop : -1.43 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 259 HIS 0.007 0.001 HIS G 54 PHE 0.022 0.001 PHE C 40 TYR 0.026 0.001 TYR E 92 ARG 0.008 0.000 ARG F 20 *********************** 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 271 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7799 (tp30) REVERT: A 178 MET cc_start: 0.6079 (mmm) cc_final: 0.5875 (mmt) REVERT: A 307 GLU cc_start: 0.7290 (tp30) cc_final: 0.6937 (tp30) REVERT: A 456 PHE cc_start: 0.7024 (t80) cc_final: 0.6729 (t80) REVERT: C 91 ASP cc_start: 0.6458 (m-30) cc_final: 0.6211 (m-30) REVERT: C 288 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4951 (m-80) REVERT: D 155 ARG cc_start: 0.5116 (tpp-160) cc_final: 0.4899 (tpt170) REVERT: F 14 ASP cc_start: 0.6474 (m-30) cc_final: 0.6016 (m-30) REVERT: F 296 TRP cc_start: 0.5791 (t60) cc_final: 0.5558 (t60) REVERT: F 468 ILE cc_start: 0.8336 (mm) cc_final: 0.7880 (mm) REVERT: G 153 SER cc_start: 0.8225 (t) cc_final: 0.7910 (m) REVERT: H 148 TYR cc_start: 0.6220 (m-80) cc_final: 0.5763 (m-80) outliers start: 38 outliers final: 24 residues processed: 259 average time/residue: 0.3505 time to fit residues: 143.9837 Evaluate side-chains 237 residues out of total 2301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0362 > 50: distance: 145 - 231: 5.428 distance: 148 - 228: 6.047 distance: 158 - 215: 36.362 distance: 161 - 212: 5.375 distance: 174 - 195: 4.642 distance: 192 - 193: 3.215 distance: 193 - 196: 4.324 distance: 194 - 195: 3.150 distance: 194 - 201: 3.004 distance: 196 - 197: 3.090 distance: 197 - 198: 4.030 distance: 198 - 199: 3.812 distance: 201 - 202: 4.748 distance: 202 - 203: 6.671 distance: 203 - 212: 3.915 distance: 205 - 206: 5.133 distance: 206 - 207: 4.824 distance: 207 - 208: 3.946 distance: 208 - 209: 6.454 distance: 209 - 211: 5.692 distance: 212 - 213: 3.395 distance: 213 - 214: 13.301 distance: 213 - 216: 8.641 distance: 214 - 215: 25.427 distance: 214 - 219: 28.317 distance: 216 - 217: 5.891 distance: 216 - 218: 4.401 distance: 219 - 220: 14.652 distance: 220 - 221: 5.269 distance: 220 - 223: 7.341 distance: 221 - 222: 4.984 distance: 221 - 228: 3.982 distance: 223 - 224: 11.326 distance: 224 - 225: 8.052 distance: 225 - 226: 13.703 distance: 225 - 227: 10.287 distance: 228 - 229: 5.447 distance: 229 - 230: 4.152 distance: 229 - 232: 4.189 distance: 230 - 240: 4.178 distance: 232 - 233: 3.065 distance: 235 - 237: 3.116 distance: 236 - 238: 3.191 distance: 242 - 243: 4.928 distance: 246 - 247: 3.002 distance: 247 - 248: 3.393 distance: 247 - 250: 3.600 distance: 248 - 249: 7.186 distance: 248 - 253: 3.622 distance: 250 - 251: 3.532 distance: 250 - 252: 6.680 distance: 253 - 254: 6.169 distance: 254 - 255: 4.733 distance: 254 - 257: 5.370 distance: 255 - 265: 5.506 distance: 257 - 258: 3.164 distance: 261 - 263: 3.797 distance: 263 - 264: 4.618 distance: 265 - 266: 4.812 distance: 266 - 267: 4.205 distance: 266 - 269: 4.582 distance: 267 - 273: 4.632 distance: 270 - 271: 6.131 distance: 270 - 272: 9.688 distance: 274 - 275: 4.436 distance: 275 - 276: 3.744 distance: 277 - 278: 4.956 distance: 277 - 279: 5.710 distance: 278 - 280: 6.766