Starting phenix.real_space_refine on Mon Mar 18 13:53:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgz_25121/03_2024/7sgz_25121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgz_25121/03_2024/7sgz_25121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgz_25121/03_2024/7sgz_25121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgz_25121/03_2024/7sgz_25121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgz_25121/03_2024/7sgz_25121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgz_25121/03_2024/7sgz_25121_updated.pdb" } resolution = 3.17 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= 0.019 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 37 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13246 2.51 5 N 3615 2.21 5 O 4038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "F PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ASP 238": "OD1" <-> "OD2" Residue "G GLU 312": "OE1" <-> "OE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21055 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3416 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 1 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: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2693 Classifications: {'peptide': 341} Modifications used: {'COO': 1} 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: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2154 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 4 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.58, per 1000 atoms: 0.55 Number of scatterers: 21055 At special positions: 0 Unit cell: (124.2, 125.028, 140.76, 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 115 16.00 P 37 15.00 Mg 4 11.99 O 4038 8.00 N 3615 7.00 C 13246 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: 8.06 Conformation dependent library (CDL) restraints added in 3.6 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 17 sheets defined 44.7% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 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 82 through 95 removed outlier: 3.736A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.759A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.703A pdb=" N PHE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) 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 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 297 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 removed outlier: 3.566A pdb=" N ILE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 376 through 386 removed outlier: 5.333A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.719A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 446 through 467 Processing helix chain 'A' and resid 476 through 482 removed outlier: 3.766A pdb=" N ILE A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.512A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) 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 74 Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.637A pdb=" N SER B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 157' 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 216 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 256 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 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.218A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' 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 205 through 218 removed outlier: 3.642A pdb=" N ALA C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) 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 270 removed outlier: 4.046A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 316 through 332 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 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 53 Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 85 through 91 removed outlier: 4.467A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 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 removed outlier: 4.393A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 208 removed outlier: 5.177A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.685A 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 229 through 245 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.838A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 149 through 160 Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 4.835A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 315 through 334 removed outlier: 3.635A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 13 through 29 removed outlier: 3.774A pdb=" N ARG F 20 " --> pdb=" O TYR F 16 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 removed outlier: 4.282A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing helix chain 'F' and resid 241 through 256 removed outlier: 3.524A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.740A pdb=" N SER F 419 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 28 removed outlier: 3.762A pdb=" N CYS G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.618A pdb=" N VAL G 93 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 94 " --> pdb=" O LEU G 90 " (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 172 removed outlier: 3.607A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 248 removed outlier: 3.619A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 329 removed outlier: 3.734A pdb=" N GLU G 325 " --> pdb=" O GLN G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 26 removed outlier: 3.917A pdb=" N ASN H 14 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE H 15 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 26 " --> pdb=" O LEU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 203 through 210 Processing helix chain 'H' and resid 234 through 243 removed outlier: 3.747A pdb=" N ASN H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 243 " --> pdb=" O ASN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 248 No H-bonds generated for 'chain 'H' and resid 246 through 248' Processing helix chain 'H' and resid 327 through 338 removed outlier: 3.552A pdb=" N PHE H 332 " --> pdb=" O ASP H 328 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE H 333 " --> pdb=" O PHE H 329 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 334 " --> pdb=" O LYS H 330 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 4.852A 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 264 removed outlier: 7.176A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.659A pdb=" N ILE B 46 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 9.055A pdb=" N LEU C 49 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE C 143 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE C 51 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 145 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY C 53 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 147 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU C 80 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.641A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 93 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.824A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN E 141 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 73 through 76 removed outlier: 3.691A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.685A pdb=" N CYS F 95 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 33 " --> pdb=" O CYS F 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.949A pdb=" N THR F 120 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.688A pdb=" N HIS F 434 " --> pdb=" O CYS F 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.910A pdb=" N ILE F 409 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 264 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS F 282 " --> pdb=" O MET F 265 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 13 through 15 removed outlier: 3.564A pdb=" N ALA G 13 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 37 through 41 removed outlier: 3.536A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.878A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.051A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 205 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.546A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 92 through 97 removed outlier: 6.908A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP H 42 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 43 " --> pdb=" O CYS H 52 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS H 52 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 371 " --> pdb=" O MET H 364 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 262 through 266 removed outlier: 3.692A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2445 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: 6.53 Time building geometry restraints manager: 8.72 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: 6902 1.36 - 1.51: 5541 1.51 - 1.66: 8844 1.66 - 1.80: 85 1.80 - 1.95: 87 Bond restraints: 21459 Sorted by residual: bond pdb=" O3 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" O2 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.567 1.511 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O1 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 99.94 - 107.17: 707 107.17 - 114.40: 13021 114.40 - 121.63: 10552 121.63 - 128.86: 4681 128.86 - 136.09: 138 Bond angle restraints: 29099 Sorted by residual: angle pdb=" CA LYS A 296 " pdb=" CB LYS A 296 " pdb=" CG LYS A 296 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" N GLU C 279 " pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 110.22 115.57 -5.35 1.54e+00 4.22e-01 1.21e+01 angle pdb=" N THR G 29 " pdb=" CA THR G 29 " pdb=" C THR G 29 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.01e+01 angle pdb=" C THR H 300 " pdb=" N LYS H 320 " pdb=" CA LYS H 320 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" CA GLY A 349 " pdb=" C GLY A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 114.23 116.71 -2.48 8.80e-01 1.29e+00 7.91e+00 ... (remaining 29094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 12708 35.06 - 70.12: 350 70.12 - 105.19: 20 105.19 - 140.25: 1 140.25 - 175.31: 1 Dihedral angle restraints: 13080 sinusoidal: 5570 harmonic: 7510 Sorted by residual: dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual 300.00 179.88 120.12 1 2.00e+01 2.50e-03 3.60e+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 35.31 -175.31 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 13077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3088 0.071 - 0.142: 269 0.142 - 0.212: 6 0.212 - 0.283: 0 0.283 - 0.354: 1 Chirality restraints: 3364 Sorted by residual: 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 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB VAL F 110 " pdb=" CA VAL F 110 " pdb=" CG1 VAL F 110 " pdb=" CG2 VAL F 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR G 29 " pdb=" N THR G 29 " pdb=" C THR G 29 " pdb=" CB THR G 29 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 3361 not shown) Planarity restraints: 3585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 298 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO F 299 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 299 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 299 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 143 " -0.009 2.00e-02 2.50e+03 1.60e-02 4.49e+00 pdb=" CG PHE C 143 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 143 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 143 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 143 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 42 " -0.012 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP H 42 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP H 42 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 42 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 42 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 42 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 42 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 42 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 42 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 42 " -0.001 2.00e-02 2.50e+03 ... (remaining 3582 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 362 2.68 - 3.24: 19884 3.24 - 3.79: 32821 3.79 - 4.35: 43382 4.35 - 4.90: 71582 Nonbonded interactions: 168031 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.128 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG E 401 " model vdw 2.136 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.141 2.170 nonbonded pdb=" O3A AGS A 701 " pdb="MG MG A 702 " model vdw 2.144 2.170 nonbonded pdb=" O2B AGS D 500 " pdb=" O3G AGS D 500 " model vdw 2.202 2.440 ... (remaining 168026 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.310 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 55.950 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 0.059 21459 Z= 0.152 Angle : 0.533 7.209 29099 Z= 0.273 Chirality : 0.040 0.354 3364 Planarity : 0.003 0.055 3585 Dihedral : 15.376 175.309 8182 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % 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: 0.10 (0.17), residues: 2516 helix: 0.92 (0.15), residues: 1167 sheet: 0.43 (0.27), residues: 453 loop : -1.22 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 42 HIS 0.009 0.001 HIS B 95 PHE 0.035 0.001 PHE C 143 TYR 0.013 0.001 TYR F 422 ARG 0.010 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 2.289 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.4026 (ppp) cc_final: 0.3670 (ptm) REVERT: F 241 GLU cc_start: 0.7240 (mp0) cc_final: 0.5624 (mp0) REVERT: F 242 PHE cc_start: 0.7400 (t80) cc_final: 0.7184 (t80) REVERT: G 36 ASP cc_start: 0.7259 (m-30) cc_final: 0.7039 (m-30) REVERT: G 64 ARG cc_start: 0.7544 (tmm-80) cc_final: 0.6512 (tpt90) REVERT: G 170 LEU cc_start: 0.7220 (tp) cc_final: 0.6916 (tp) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.3368 time to fit residues: 163.0445 Evaluate side-chains 247 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 148 optimal weight: 0.0270 chunk 230 optimal weight: 6.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS B 64 HIS B 79 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 127 GLN C 148 ASN D 305 HIS D 340 HIS D 352 GLN G 52 ASN G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21459 Z= 0.337 Angle : 0.641 7.840 29099 Z= 0.329 Chirality : 0.045 0.208 3364 Planarity : 0.005 0.057 3585 Dihedral : 12.344 176.136 3076 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 1.51 % Allowed : 10.42 % Favored : 88.07 % 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: 2516 helix: 0.71 (0.15), residues: 1172 sheet: 0.15 (0.25), residues: 484 loop : -1.36 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.008 0.001 HIS C 260 PHE 0.025 0.002 PHE A 443 TYR 0.017 0.002 TYR A 339 ARG 0.007 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 277 time to evaluate : 2.355 Fit side-chains REVERT: C 284 ILE cc_start: 0.8807 (tt) cc_final: 0.8522 (mp) REVERT: E 1 MET cc_start: 0.4601 (ppp) cc_final: 0.4356 (ptm) REVERT: E 71 ASP cc_start: 0.7430 (p0) cc_final: 0.7015 (p0) REVERT: F 241 GLU cc_start: 0.7070 (mp0) cc_final: 0.5885 (mp0) REVERT: F 411 ARG cc_start: 0.7312 (ptm-80) cc_final: 0.6954 (ptm160) REVERT: G 36 ASP cc_start: 0.7394 (m-30) cc_final: 0.7188 (m-30) REVERT: G 121 PHE cc_start: 0.6768 (m-80) cc_final: 0.6407 (m-80) REVERT: G 231 PHE cc_start: 0.8238 (t80) cc_final: 0.8023 (t80) REVERT: H 253 LYS cc_start: 0.7136 (ttpp) cc_final: 0.6147 (mtpt) outliers start: 35 outliers final: 25 residues processed: 298 average time/residue: 0.3381 time to fit residues: 154.1929 Evaluate side-chains 260 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 0.0980 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 231 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 185 optimal weight: 10.0000 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 148 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN D 305 HIS E 110 GLN G 52 ASN ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21459 Z= 0.145 Angle : 0.490 6.832 29099 Z= 0.252 Chirality : 0.039 0.208 3364 Planarity : 0.003 0.052 3585 Dihedral : 11.997 174.518 3076 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.77 % Allowed : 12.88 % Favored : 85.34 % 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: 0.16 (0.17), residues: 2516 helix: 1.11 (0.16), residues: 1171 sheet: 0.29 (0.25), residues: 471 loop : -1.35 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 256 HIS 0.010 0.001 HIS D 305 PHE 0.014 0.001 PHE A 456 TYR 0.013 0.001 TYR C 52 ARG 0.005 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 241 time to evaluate : 2.926 Fit side-chains revert: symmetry clash REVERT: C 50 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8057 (tp) REVERT: D 88 MET cc_start: 0.6005 (mmt) cc_final: 0.5756 (mmp) REVERT: F 241 GLU cc_start: 0.7061 (mp0) cc_final: 0.5870 (mp0) REVERT: G 36 ASP cc_start: 0.7400 (m-30) cc_final: 0.7185 (m-30) REVERT: G 121 PHE cc_start: 0.6759 (m-80) cc_final: 0.6482 (m-80) REVERT: G 231 PHE cc_start: 0.8171 (t80) cc_final: 0.7935 (t80) outliers start: 41 outliers final: 25 residues processed: 266 average time/residue: 0.3196 time to fit residues: 132.7482 Evaluate side-chains 257 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 231 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 219 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 244 ASN G 52 ASN G 53 ASN ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21459 Z= 0.203 Angle : 0.506 6.570 29099 Z= 0.260 Chirality : 0.040 0.228 3364 Planarity : 0.003 0.054 3585 Dihedral : 12.028 174.971 3076 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.64 % Allowed : 14.44 % Favored : 83.92 % 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: 0.10 (0.17), residues: 2516 helix: 1.08 (0.16), residues: 1181 sheet: 0.08 (0.25), residues: 479 loop : -1.34 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.010 0.001 HIS D 305 PHE 0.013 0.001 PHE F 160 TYR 0.014 0.001 TYR C 52 ARG 0.004 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8188 (tp) REVERT: C 77 ASN cc_start: 0.7736 (t0) cc_final: 0.7414 (t0) REVERT: F 241 GLU cc_start: 0.7136 (mp0) cc_final: 0.6000 (mp0) REVERT: G 36 ASP cc_start: 0.7389 (m-30) cc_final: 0.7143 (m-30) REVERT: G 40 PHE cc_start: 0.7488 (m-80) cc_final: 0.7000 (m-80) REVERT: G 155 GLU cc_start: 0.7778 (pp20) cc_final: 0.7522 (pt0) REVERT: G 231 PHE cc_start: 0.8180 (t80) cc_final: 0.7922 (t80) outliers start: 38 outliers final: 29 residues processed: 260 average time/residue: 0.3339 time to fit residues: 134.6940 Evaluate side-chains 255 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 475 HIS ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 144 ASN E 244 ASN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 53 ASN G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21459 Z= 0.248 Angle : 0.544 8.403 29099 Z= 0.279 Chirality : 0.042 0.172 3364 Planarity : 0.004 0.053 3585 Dihedral : 12.114 175.192 3076 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.72 % Allowed : 15.18 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2516 helix: 0.92 (0.15), residues: 1181 sheet: -0.03 (0.24), residues: 477 loop : -1.42 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 290 HIS 0.006 0.001 HIS C 184 PHE 0.018 0.002 PHE F 160 TYR 0.015 0.001 TYR A 471 ARG 0.005 0.000 ARG E 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 261 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7679 (mt) REVERT: C 50 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (tp) REVERT: C 77 ASN cc_start: 0.7959 (t0) cc_final: 0.7745 (t0) REVERT: C 284 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8415 (mp) REVERT: F 241 GLU cc_start: 0.7267 (mp0) cc_final: 0.6364 (mp0) REVERT: G 36 ASP cc_start: 0.7507 (m-30) cc_final: 0.7243 (m-30) REVERT: G 40 PHE cc_start: 0.7368 (m-80) cc_final: 0.6943 (m-80) REVERT: G 155 GLU cc_start: 0.7943 (pp20) cc_final: 0.7589 (pt0) REVERT: G 231 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7901 (t80) outliers start: 63 outliers final: 45 residues processed: 300 average time/residue: 0.3354 time to fit residues: 155.0139 Evaluate side-chains 285 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 236 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 204 optimal weight: 0.0970 chunk 113 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21459 Z= 0.162 Angle : 0.495 7.170 29099 Z= 0.255 Chirality : 0.040 0.215 3364 Planarity : 0.003 0.052 3585 Dihedral : 11.942 174.623 3076 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.29 % Allowed : 17.12 % Favored : 80.59 % 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: 0.09 (0.17), residues: 2516 helix: 1.17 (0.16), residues: 1166 sheet: -0.12 (0.24), residues: 478 loop : -1.31 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 4 HIS 0.006 0.001 HIS B 95 PHE 0.013 0.001 PHE F 160 TYR 0.013 0.001 TYR C 52 ARG 0.005 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7617 (mmtm) cc_final: 0.7025 (pttt) REVERT: A 475 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.4522 (m90) REVERT: B 294 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7657 (mt) REVERT: C 284 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8276 (mp) REVERT: F 241 GLU cc_start: 0.7240 (mp0) cc_final: 0.6304 (mp0) REVERT: G 36 ASP cc_start: 0.7374 (m-30) cc_final: 0.7111 (m-30) REVERT: G 40 PHE cc_start: 0.7365 (m-80) cc_final: 0.6936 (m-80) REVERT: G 155 GLU cc_start: 0.7942 (pp20) cc_final: 0.7572 (pt0) REVERT: G 231 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7925 (t80) REVERT: H 268 LYS cc_start: 0.7965 (tppt) cc_final: 0.6891 (tttm) outliers start: 53 outliers final: 35 residues processed: 282 average time/residue: 0.3296 time to fit residues: 144.0099 Evaluate side-chains 274 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 206 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 153 optimal weight: 0.0070 chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 53 ASN ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21459 Z= 0.204 Angle : 0.514 7.979 29099 Z= 0.263 Chirality : 0.041 0.196 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.965 174.987 3076 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.85 % Allowed : 16.86 % Favored : 80.29 % 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: 0.08 (0.17), residues: 2516 helix: 1.18 (0.16), residues: 1163 sheet: -0.12 (0.24), residues: 478 loop : -1.33 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 4 HIS 0.005 0.001 HIS B 95 PHE 0.015 0.001 PHE G 31 TYR 0.019 0.001 TYR E 8 ARG 0.005 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 244 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7057 (pttt) REVERT: C 284 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8241 (mp) REVERT: F 41 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.6030 (mtt-85) REVERT: F 241 GLU cc_start: 0.7270 (mp0) cc_final: 0.6327 (mp0) REVERT: G 36 ASP cc_start: 0.7381 (m-30) cc_final: 0.7113 (m-30) REVERT: G 40 PHE cc_start: 0.7421 (m-80) cc_final: 0.7001 (m-80) REVERT: G 135 TYR cc_start: 0.8526 (m-80) cc_final: 0.8257 (m-80) REVERT: G 155 GLU cc_start: 0.7931 (pp20) cc_final: 0.7558 (pt0) REVERT: G 231 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (t80) REVERT: H 268 LYS cc_start: 0.8000 (tppt) cc_final: 0.6933 (tttm) outliers start: 66 outliers final: 49 residues processed: 290 average time/residue: 0.3169 time to fit residues: 144.2368 Evaluate side-chains 284 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 192 optimal weight: 8.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21459 Z= 0.183 Angle : 0.512 7.721 29099 Z= 0.261 Chirality : 0.040 0.167 3364 Planarity : 0.003 0.052 3585 Dihedral : 11.904 174.745 3076 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.38 % Allowed : 17.51 % Favored : 80.11 % 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: 0.16 (0.17), residues: 2516 helix: 1.25 (0.16), residues: 1154 sheet: -0.09 (0.24), residues: 478 loop : -1.28 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 4 HIS 0.007 0.001 HIS B 95 PHE 0.018 0.001 PHE A 364 TYR 0.014 0.001 TYR C 52 ARG 0.005 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 232 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 284 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8210 (mp) REVERT: F 241 GLU cc_start: 0.7260 (mp0) cc_final: 0.6295 (mp0) REVERT: G 36 ASP cc_start: 0.7382 (m-30) cc_final: 0.7138 (m-30) REVERT: G 40 PHE cc_start: 0.7406 (m-80) cc_final: 0.7009 (m-80) REVERT: G 135 TYR cc_start: 0.8496 (m-80) cc_final: 0.8232 (m-80) REVERT: G 155 GLU cc_start: 0.8002 (pp20) cc_final: 0.7651 (pt0) REVERT: G 231 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7981 (t80) REVERT: H 268 LYS cc_start: 0.7991 (tppt) cc_final: 0.6930 (tttm) outliers start: 55 outliers final: 47 residues processed: 271 average time/residue: 0.3135 time to fit residues: 134.0308 Evaluate side-chains 273 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 224 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 203 HIS G 53 ASN G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21459 Z= 0.335 Angle : 0.610 10.315 29099 Z= 0.313 Chirality : 0.044 0.252 3364 Planarity : 0.004 0.057 3585 Dihedral : 12.186 175.688 3076 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.55 % Allowed : 17.60 % Favored : 79.85 % 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: -0.27 (0.17), residues: 2516 helix: 0.84 (0.15), residues: 1163 sheet: -0.33 (0.24), residues: 486 loop : -1.41 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 295 HIS 0.006 0.001 HIS B 95 PHE 0.023 0.002 PHE F 160 TYR 0.019 0.002 TYR H 64 ARG 0.005 0.001 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 246 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.6198 (p90) REVERT: C 284 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8359 (mp) REVERT: F 231 MET cc_start: 0.4514 (tmm) cc_final: 0.3635 (tpp) REVERT: F 241 GLU cc_start: 0.7306 (mp0) cc_final: 0.6875 (mp0) REVERT: G 36 ASP cc_start: 0.7521 (m-30) cc_final: 0.7226 (m-30) REVERT: G 40 PHE cc_start: 0.7436 (m-80) cc_final: 0.7009 (m-80) REVERT: G 96 MET cc_start: 0.5687 (pmm) cc_final: 0.4810 (mmm) REVERT: G 155 GLU cc_start: 0.7998 (pp20) cc_final: 0.7644 (pt0) REVERT: G 231 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8019 (t80) REVERT: H 262 SER cc_start: 0.8385 (t) cc_final: 0.7995 (m) outliers start: 59 outliers final: 50 residues processed: 288 average time/residue: 0.3159 time to fit residues: 142.0152 Evaluate side-chains 290 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN G 53 ASN G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21459 Z= 0.207 Angle : 0.537 8.746 29099 Z= 0.275 Chirality : 0.041 0.228 3364 Planarity : 0.003 0.052 3585 Dihedral : 11.980 174.781 3076 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.38 % Allowed : 18.07 % Favored : 79.55 % 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: 2516 helix: 1.02 (0.16), residues: 1161 sheet: -0.35 (0.24), residues: 487 loop : -1.38 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 4 HIS 0.009 0.001 HIS B 64 PHE 0.018 0.001 PHE G 31 TYR 0.014 0.001 TYR C 52 ARG 0.006 0.000 ARG E 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 284 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8337 (mp) REVERT: F 108 ASP cc_start: 0.7976 (m-30) cc_final: 0.7749 (m-30) REVERT: F 231 MET cc_start: 0.4519 (tmm) cc_final: 0.3570 (tpp) REVERT: F 241 GLU cc_start: 0.7263 (mp0) cc_final: 0.6825 (mp0) REVERT: G 36 ASP cc_start: 0.7462 (m-30) cc_final: 0.7158 (m-30) REVERT: G 96 MET cc_start: 0.5689 (pmm) cc_final: 0.5143 (mmm) REVERT: G 135 TYR cc_start: 0.8548 (m-80) cc_final: 0.8298 (m-80) REVERT: G 155 GLU cc_start: 0.7986 (pp20) cc_final: 0.7629 (pt0) REVERT: G 231 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8050 (t80) REVERT: H 262 SER cc_start: 0.8374 (t) cc_final: 0.7983 (m) outliers start: 55 outliers final: 46 residues processed: 278 average time/residue: 0.3183 time to fit residues: 137.9268 Evaluate side-chains 278 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 185 optimal weight: 30.0000 chunk 29 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130269 restraints weight = 27603.491| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.64 r_work: 0.3534 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21459 Z= 0.164 Angle : 0.511 9.367 29099 Z= 0.261 Chirality : 0.040 0.212 3364 Planarity : 0.003 0.052 3585 Dihedral : 11.814 174.453 3076 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.12 % Allowed : 18.33 % Favored : 79.55 % 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: 0.07 (0.17), residues: 2516 helix: 1.23 (0.16), residues: 1153 sheet: -0.27 (0.24), residues: 486 loop : -1.30 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 4 HIS 0.011 0.001 HIS B 64 PHE 0.013 0.001 PHE A 364 TYR 0.014 0.001 TYR C 52 ARG 0.006 0.000 ARG E 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4444.90 seconds wall clock time: 83 minutes 45.71 seconds (5025.71 seconds total)