Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 14:14:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/04_2023/6wdn_21642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/04_2023/6wdn_21642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/04_2023/6wdn_21642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/04_2023/6wdn_21642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/04_2023/6wdn_21642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/04_2023/6wdn_21642.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.043 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8151 2.51 5 N 2129 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 89": "NH1" <-> "NH2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "I ASP 178": "OD1" <-> "OD2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 288": "OE1" <-> "OE2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I ARG 295": "NH1" <-> "NH2" Residue "I TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 313": "OD1" <-> "OD2" Residue "E TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 330": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12612 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2539 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2833 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1453 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 4, 'TRANS': 168} Chain: "D" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1463 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "H" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1354 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "J" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 354 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1462 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Time building chain proxies: 6.95, per 1000 atoms: 0.55 Number of scatterers: 12612 At special positions: 0 Unit cell: (84.8, 98.58, 185.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2264 8.00 N 2129 7.00 C 8151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS B 463 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 4 sheets defined 72.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.611A pdb=" N PHE A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 4.029A pdb=" N PHE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.505A pdb=" N ASP A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.504A pdb=" N THR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.016A pdb=" N HIS A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.869A pdb=" N PHE A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.582A pdb=" N MET A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 272 removed outlier: 3.559A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.620A pdb=" N PHE A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 4.509A pdb=" N ASP A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.589A pdb=" N ILE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.552A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 4.073A pdb=" N LEU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.768A pdb=" N GLN A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TRP A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.834A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.566A pdb=" N PHE B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.836A pdb=" N PHE B 223 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.937A pdb=" N GLN B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 6.575A pdb=" N MET B 256 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 293 through 314 removed outlier: 3.504A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.709A pdb=" N GLN B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 removed outlier: 3.824A pdb=" N PHE B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 4.920A pdb=" N THR B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.661A pdb=" N GLN B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 4.134A pdb=" N PHE B 417 " --> pdb=" O CYS B 413 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.840A pdb=" N SER B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.304A pdb=" N ALA B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 70 through 90 Proline residue: F 76 - end of helix removed outlier: 3.576A pdb=" N THR F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'C' and resid 174 through 190 removed outlier: 3.648A pdb=" N THR C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 removed outlier: 3.690A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.566A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.067A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 241 removed outlier: 3.764A pdb=" N ARG C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 253 removed outlier: 4.163A pdb=" N PHE C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.877A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 286 Processing helix chain 'C' and resid 290 through 311 removed outlier: 3.860A pdb=" N ASP C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.714A pdb=" N GLN C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 75 through 93 removed outlier: 3.660A pdb=" N VAL D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 190 removed outlier: 4.226A pdb=" N ASP G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL G 179 " --> pdb=" O THR G 175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 228 removed outlier: 4.541A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 204 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU G 208 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 210 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 4.324A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG G 226 " --> pdb=" O ILE G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 249 removed outlier: 3.664A pdb=" N MET G 243 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 256 removed outlier: 3.898A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 Processing helix chain 'G' and resid 265 through 270 Processing helix chain 'G' and resid 270 through 275 removed outlier: 3.662A pdb=" N ALA G 275 " --> pdb=" O THR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 Processing helix chain 'G' and resid 290 through 310 removed outlier: 4.462A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE G 302 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 310 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 340 removed outlier: 3.652A pdb=" N ALA G 323 " --> pdb=" O GLN G 319 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU G 328 " --> pdb=" O ILE G 324 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP G 336 " --> pdb=" O LYS G 332 " (cutoff:3.500A) Proline residue: G 337 - end of helix Processing helix chain 'H' and resid 65 through 73 removed outlier: 3.501A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 93 removed outlier: 3.559A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 189 removed outlier: 3.788A pdb=" N LEU I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN I 184 " --> pdb=" O LYS I 180 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 225 removed outlier: 3.570A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU I 205 " --> pdb=" O ARG I 201 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU I 210 " --> pdb=" O ARG I 206 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) Proline residue: I 216 - end of helix removed outlier: 4.287A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU I 223 " --> pdb=" O LYS I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 232 Processing helix chain 'I' and resid 233 through 254 removed outlier: 3.570A pdb=" N TRP I 237 " --> pdb=" O THR I 233 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE I 247 " --> pdb=" O MET I 243 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 275 No H-bonds generated for 'chain 'I' and resid 273 through 275' Processing helix chain 'I' and resid 276 through 281 Processing helix chain 'I' and resid 281 through 286 Processing helix chain 'I' and resid 290 through 311 removed outlier: 3.782A pdb=" N GLN I 298 " --> pdb=" O ALA I 294 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 305 " --> pdb=" O LEU I 301 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS I 309 " --> pdb=" O LYS I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 330 removed outlier: 3.710A pdb=" N ALA I 323 " --> pdb=" O GLN I 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 74 through 79 Processing helix chain 'J' and resid 79 through 93 removed outlier: 3.999A pdb=" N SER J 85 " --> pdb=" O GLY J 81 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE J 88 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 190 removed outlier: 3.557A pdb=" N THR E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 removed outlier: 4.186A pdb=" N LEU E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 199 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 219 removed outlier: 3.593A pdb=" N ALA E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.524A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 248 removed outlier: 3.864A pdb=" N ARG E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.606A pdb=" N MET E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'E' and resid 290 through 310 removed outlier: 3.536A pdb=" N ASP E 296 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 306 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 335 removed outlier: 4.143A pdb=" N ASP E 322 " --> pdb=" O ASN E 318 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.536A pdb=" N LYS B 174 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 238 609 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2038 1.31 - 1.44: 3504 1.44 - 1.57: 7215 1.57 - 1.71: 0 1.71 - 1.84: 123 Bond restraints: 12880 Sorted by residual: bond pdb=" C SER H 72 " pdb=" O SER H 72 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.17e-02 7.31e+03 2.64e+01 bond pdb=" C PRO H 76 " pdb=" O PRO H 76 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.26e-02 6.30e+03 2.60e+01 bond pdb=" CA SER H 72 " pdb=" CB SER H 72 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.56e-02 4.11e+03 1.81e+01 bond pdb=" C TYR H 79 " pdb=" O TYR H 79 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.19e-02 7.06e+03 1.80e+01 bond pdb=" C ARG B 259 " pdb=" O ARG B 259 " ideal model delta sigma weight residual 1.232 1.185 0.047 1.12e-02 7.97e+03 1.76e+01 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.43: 286 106.43 - 113.33: 6921 113.33 - 120.23: 5115 120.23 - 127.12: 4909 127.12 - 134.02: 113 Bond angle restraints: 17344 Sorted by residual: angle pdb=" N VAL H 80 " pdb=" CA VAL H 80 " pdb=" C VAL H 80 " ideal model delta sigma weight residual 113.00 103.88 9.12 1.30e+00 5.92e-01 4.92e+01 angle pdb=" N ARG B 259 " pdb=" CA ARG B 259 " pdb=" C ARG B 259 " ideal model delta sigma weight residual 109.83 99.74 10.09 1.55e+00 4.16e-01 4.24e+01 angle pdb=" C PRO H 76 " pdb=" CA PRO H 76 " pdb=" CB PRO H 76 " ideal model delta sigma weight residual 112.62 102.28 10.34 1.65e+00 3.67e-01 3.92e+01 angle pdb=" CA PHE H 77 " pdb=" CB PHE H 77 " pdb=" CG PHE H 77 " ideal model delta sigma weight residual 113.80 107.75 6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" C ARG B 259 " pdb=" N HIS B 260 " pdb=" CA HIS B 260 " ideal model delta sigma weight residual 121.87 111.03 10.84 1.83e+00 2.99e-01 3.51e+01 ... (remaining 17339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 6838 17.53 - 35.07: 735 35.07 - 52.60: 151 52.60 - 70.14: 22 70.14 - 87.67: 12 Dihedral angle restraints: 7758 sinusoidal: 3230 harmonic: 4528 Sorted by residual: dihedral pdb=" CB CYS A 413 " pdb=" SG CYS A 413 " pdb=" SG CYS B 463 " pdb=" CB CYS B 463 " ideal model delta sinusoidal sigma weight residual -86.00 -30.71 -55.29 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CD ARG B 261 " pdb=" NE ARG B 261 " pdb=" CZ ARG B 261 " pdb=" NH1 ARG B 261 " ideal model delta sinusoidal sigma weight residual 0.00 49.62 -49.62 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" C PRO H 76 " pdb=" N PRO H 76 " pdb=" CA PRO H 76 " pdb=" CB PRO H 76 " ideal model delta harmonic sigma weight residual -120.70 -107.65 -13.05 0 2.50e+00 1.60e-01 2.73e+01 ... (remaining 7755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1815 0.088 - 0.177: 76 0.177 - 0.265: 11 0.265 - 0.354: 4 0.354 - 0.442: 1 Chirality restraints: 1907 Sorted by residual: chirality pdb=" CA SER B 276 " pdb=" N SER B 276 " pdb=" C SER B 276 " pdb=" CB SER B 276 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA VAL H 70 " pdb=" N VAL H 70 " pdb=" C VAL H 70 " pdb=" CB VAL H 70 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ARG H 69 " pdb=" N ARG H 69 " pdb=" C ARG H 69 " pdb=" CB ARG H 69 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1904 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 261 " 0.843 9.50e-02 1.11e+02 3.78e-01 8.67e+01 pdb=" NE ARG B 261 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 261 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 261 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 261 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 69 " 0.466 9.50e-02 1.11e+02 2.09e-01 2.66e+01 pdb=" NE ARG H 69 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 69 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG H 69 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 69 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 77 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PHE H 77 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE H 77 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU H 78 " -0.025 2.00e-02 2.50e+03 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 599 2.71 - 3.26: 14288 3.26 - 3.81: 19900 3.81 - 4.35: 25722 4.35 - 4.90: 40353 Nonbonded interactions: 100862 Sorted by model distance: nonbonded pdb=" OG SER A 363 " pdb=" OD1 ASN A 365 " model vdw 2.166 2.440 nonbonded pdb=" OE2 GLU B 115 " pdb=" OH TYR B 130 " model vdw 2.172 2.440 nonbonded pdb=" OG SER C 225 " pdb=" OH TYR C 299 " model vdw 2.193 2.440 nonbonded pdb=" O GLN A 336 " pdb=" OG SER A 339 " model vdw 2.214 2.440 nonbonded pdb=" O ASP B 392 " pdb=" OG1 THR B 395 " model vdw 2.218 2.440 ... (remaining 100857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 177 through 336) selection = (chain 'E' and resid 177 through 336) selection = (chain 'G' and resid 177 through 336) selection = chain 'I' } ncs_group { reference = (chain 'D' and resid 48 through 93) selection = (chain 'F' and resid 48 through 93) selection = (chain 'H' and resid 48 through 93) selection = chain 'J' } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.810 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 33.860 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.005 0.066 12880 Z= 0.328 Angle : 0.741 11.137 17344 Z= 0.461 Chirality : 0.048 0.442 1907 Planarity : 0.010 0.378 2185 Dihedral : 15.067 87.671 4819 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.14 % 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: -5.36 (0.16), residues: 1516 helix: -3.67 (0.11), residues: 1052 sheet: -4.70 (0.94), residues: 14 loop : -2.56 (0.28), residues: 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 261 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 267 average time/residue: 0.2644 time to fit residues: 99.5224 Evaluate side-chains 186 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1089 time to fit residues: 3.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 260 GLN A 295 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 408 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN B 439 GLN C 198 ASN C 287 GLN G 196 GLN I 304 HIS ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 287 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12880 Z= 0.185 Angle : 0.621 8.710 17344 Z= 0.322 Chirality : 0.041 0.186 1907 Planarity : 0.004 0.059 2185 Dihedral : 5.062 22.259 1685 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.41 % 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: -3.55 (0.19), residues: 1516 helix: -2.24 (0.14), residues: 1077 sheet: -3.43 (1.73), residues: 10 loop : -2.06 (0.28), residues: 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 1.738 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 232 average time/residue: 0.2287 time to fit residues: 79.0852 Evaluate side-chains 201 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1167 time to fit residues: 4.2000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 0.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12880 Z= 0.191 Angle : 0.593 11.350 17344 Z= 0.305 Chirality : 0.041 0.200 1907 Planarity : 0.004 0.054 2185 Dihedral : 4.855 22.327 1685 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.85 % 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: -2.72 (0.20), residues: 1516 helix: -1.58 (0.15), residues: 1080 sheet: -3.19 (1.76), residues: 10 loop : -1.87 (0.29), residues: 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 228 average time/residue: 0.2275 time to fit residues: 76.9095 Evaluate side-chains 208 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1193 time to fit residues: 4.8330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 129 optimal weight: 0.0670 chunk 39 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12880 Z= 0.167 Angle : 0.591 12.930 17344 Z= 0.297 Chirality : 0.040 0.212 1907 Planarity : 0.004 0.054 2185 Dihedral : 4.640 21.098 1685 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.00 % 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: -2.12 (0.21), residues: 1516 helix: -1.10 (0.15), residues: 1074 sheet: -3.29 (1.69), residues: 10 loop : -1.75 (0.29), residues: 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 223 average time/residue: 0.2240 time to fit residues: 75.0444 Evaluate side-chains 199 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.682 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1240 time to fit residues: 5.6981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 12880 Z= 0.343 Angle : 0.668 11.916 17344 Z= 0.339 Chirality : 0.044 0.187 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.863 23.103 1685 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1516 helix: -0.97 (0.15), residues: 1081 sheet: -3.26 (1.29), residues: 14 loop : -1.77 (0.29), residues: 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 215 average time/residue: 0.2159 time to fit residues: 70.6573 Evaluate side-chains 200 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1148 time to fit residues: 5.8292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN G 184 GLN ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12880 Z= 0.201 Angle : 0.619 12.329 17344 Z= 0.312 Chirality : 0.041 0.253 1907 Planarity : 0.004 0.054 2185 Dihedral : 4.679 21.626 1685 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1516 helix: -0.72 (0.16), residues: 1096 sheet: -3.13 (1.30), residues: 14 loop : -1.64 (0.30), residues: 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 200 average time/residue: 0.2327 time to fit residues: 70.6782 Evaluate side-chains 187 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 1.708 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1502 time to fit residues: 4.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12880 Z= 0.202 Angle : 0.628 9.452 17344 Z= 0.316 Chirality : 0.041 0.223 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.624 21.737 1685 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1516 helix: -0.51 (0.16), residues: 1087 sheet: -3.18 (1.29), residues: 14 loop : -1.61 (0.31), residues: 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 203 average time/residue: 0.2170 time to fit residues: 66.6506 Evaluate side-chains 189 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.603 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1153 time to fit residues: 4.0596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12880 Z= 0.191 Angle : 0.635 10.096 17344 Z= 0.317 Chirality : 0.041 0.247 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.566 21.392 1685 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.59 % 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: -1.23 (0.22), residues: 1516 helix: -0.40 (0.16), residues: 1094 sheet: -3.16 (1.29), residues: 14 loop : -1.53 (0.31), residues: 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 193 average time/residue: 0.2338 time to fit residues: 67.6421 Evaluate side-chains 184 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1258 time to fit residues: 2.8069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 142 optimal weight: 0.0870 chunk 86 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN I 177 ASN E 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 12880 Z= 0.184 Angle : 0.646 11.046 17344 Z= 0.322 Chirality : 0.041 0.252 1907 Planarity : 0.003 0.050 2185 Dihedral : 4.505 21.171 1685 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1516 helix: -0.27 (0.16), residues: 1098 sheet: -3.04 (1.30), residues: 14 loop : -1.49 (0.31), residues: 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 195 average time/residue: 0.2241 time to fit residues: 66.6153 Evaluate side-chains 187 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.762 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1222 time to fit residues: 3.7568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 0.0020 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12880 Z= 0.233 Angle : 0.674 12.208 17344 Z= 0.337 Chirality : 0.043 0.246 1907 Planarity : 0.004 0.052 2185 Dihedral : 4.572 22.344 1685 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.59 % 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: -1.00 (0.22), residues: 1516 helix: -0.20 (0.16), residues: 1098 sheet: -3.03 (1.33), residues: 14 loop : -1.54 (0.31), residues: 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 191 average time/residue: 0.2315 time to fit residues: 67.0103 Evaluate side-chains 185 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.703 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1218 time to fit residues: 3.2858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.100753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071854 restraints weight = 30333.731| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.97 r_work: 0.3183 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12880 Z= 0.201 Angle : 0.664 12.362 17344 Z= 0.332 Chirality : 0.042 0.245 1907 Planarity : 0.004 0.050 2185 Dihedral : 4.537 21.041 1685 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.59 % 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: -0.82 (0.22), residues: 1516 helix: -0.06 (0.16), residues: 1095 sheet: -2.89 (1.36), residues: 14 loop : -1.49 (0.31), residues: 407 =============================================================================== Job complete usr+sys time: 2682.10 seconds wall clock time: 49 minutes 41.44 seconds (2981.44 seconds total)