Starting phenix.real_space_refine on Fri Mar 15 19:38:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/03_2024/6wdn_21642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/03_2024/6wdn_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_21642/03_2024/6wdn_21642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/03_2024/6wdn_21642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/03_2024/6wdn_21642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdn_21642/03_2024/6wdn_21642.pdb" } resolution = 3.2 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= 0.043 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-dev-5265/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: 7.16, per 1000 atoms: 0.57 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: 4.91 Conformation dependent library (CDL) restraints added in 2.1 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: 1.07 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: 2.97 Time building geometry restraints manager: 5.29 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: 2.500 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: 10.370 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 34.060 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.750 ------------------------------------------------------------------------------- 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 % Allowed : 6.60 % Favored : 92.88 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 256 HIS 0.016 0.001 HIS B 260 PHE 0.015 0.001 PHE C 312 TYR 0.031 0.001 TYR H 79 ARG 0.008 0.000 ARG E 252 *********************** 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 : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8265 (mtp) cc_final: 0.8050 (mtp) REVERT: A 103 TYR cc_start: 0.7299 (m-80) cc_final: 0.6424 (m-80) REVERT: A 189 ASN cc_start: 0.8940 (t0) cc_final: 0.8489 (p0) REVERT: A 295 ASN cc_start: 0.9094 (t0) cc_final: 0.8763 (t0) REVERT: B 463 CYS cc_start: 0.6990 (t) cc_final: 0.6633 (t) REVERT: C 257 GLU cc_start: 0.8352 (tp30) cc_final: 0.7981 (tp30) REVERT: C 329 MET cc_start: 0.8640 (tpt) cc_final: 0.8349 (tpp) REVERT: I 329 MET cc_start: 0.8234 (tmm) cc_final: 0.8023 (tmm) REVERT: J 86 LYS cc_start: 0.8011 (tmmt) cc_final: 0.7754 (ttmt) REVERT: E 329 MET cc_start: 0.8735 (tmm) cc_final: 0.8485 (tpp) outliers start: 7 outliers final: 5 residues processed: 267 average time/residue: 0.2623 time to fit residues: 98.9222 Evaluate side-chains 190 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain H residue 76 PRO 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: 0.0270 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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: 0.7947 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12880 Z= 0.183 Angle : 0.617 8.735 17344 Z= 0.321 Chirality : 0.041 0.188 1907 Planarity : 0.004 0.059 2185 Dihedral : 5.179 33.118 1694 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.41 % Allowed : 14.99 % Favored : 83.61 % 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: -2.23 (0.13), residues: 1077 sheet: -3.45 (1.73), residues: 10 loop : -2.08 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.006 0.001 HIS E 304 PHE 0.026 0.001 PHE E 312 TYR 0.014 0.001 TYR E 258 ARG 0.006 0.000 ARG B 261 *********************** 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 245 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 226 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7205 (m-80) cc_final: 0.6539 (m-80) REVERT: A 104 MET cc_start: 0.6022 (tpp) cc_final: 0.5664 (tpp) REVERT: A 183 MET cc_start: 0.8706 (ptm) cc_final: 0.8448 (ptm) REVERT: A 295 ASN cc_start: 0.8829 (t160) cc_final: 0.8504 (t0) REVERT: B 384 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 413 CYS cc_start: 0.8514 (m) cc_final: 0.8024 (m) REVERT: B 463 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6949 (t) REVERT: C 243 MET cc_start: 0.8791 (ttm) cc_final: 0.8466 (ttm) REVERT: C 257 GLU cc_start: 0.8282 (tp30) cc_final: 0.8060 (tp30) REVERT: C 313 ASP cc_start: 0.8386 (t0) cc_final: 0.6433 (t0) REVERT: G 187 TYR cc_start: 0.8713 (t80) cc_final: 0.8277 (t80) REVERT: G 212 GLU cc_start: 0.8524 (pp20) cc_final: 0.8324 (pp20) REVERT: G 222 ILE cc_start: 0.9044 (tp) cc_final: 0.8720 (tp) REVERT: G 243 MET cc_start: 0.7909 (ttm) cc_final: 0.7630 (ttm) REVERT: G 270 ILE cc_start: 0.8836 (mm) cc_final: 0.8628 (mt) REVERT: G 329 MET cc_start: 0.8560 (ppp) cc_final: 0.8178 (ppp) REVERT: G 330 ASP cc_start: 0.8046 (m-30) cc_final: 0.7796 (m-30) REVERT: I 246 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8388 (tm-30) REVERT: I 293 GLU cc_start: 0.8099 (mp0) cc_final: 0.7777 (mp0) REVERT: I 328 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8315 (mm-30) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 0.2212 time to fit residues: 76.7193 Evaluate side-chains 207 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.2642 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= 0.218 Angle : 0.601 10.674 17344 Z= 0.310 Chirality : 0.041 0.202 1907 Planarity : 0.004 0.055 2185 Dihedral : 5.016 34.627 1687 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.74 % Allowed : 17.73 % Favored : 79.53 % 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: -2.73 (0.20), residues: 1516 helix: -1.59 (0.15), residues: 1079 sheet: -3.23 (1.76), residues: 10 loop : -1.88 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.006 0.001 HIS E 304 PHE 0.020 0.001 PHE G 247 TYR 0.015 0.001 TYR E 299 ARG 0.005 0.000 ARG C 311 *********************** 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 250 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7250 (m-80) cc_final: 0.6606 (m-80) REVERT: A 278 MET cc_start: 0.7054 (ppp) cc_final: 0.6691 (ppp) REVERT: A 295 ASN cc_start: 0.8837 (t160) cc_final: 0.8540 (t0) REVERT: B 271 LYS cc_start: 0.8284 (mtmm) cc_final: 0.8007 (mtmm) REVERT: B 311 GLU cc_start: 0.8025 (tt0) cc_final: 0.7537 (tm-30) REVERT: B 384 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8302 (t80) REVERT: B 413 CYS cc_start: 0.8471 (m) cc_final: 0.7964 (m) REVERT: B 442 MET cc_start: 0.8432 (ptp) cc_final: 0.8214 (pmm) REVERT: B 463 CYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7039 (t) REVERT: C 257 GLU cc_start: 0.8260 (tp30) cc_final: 0.7990 (tp30) REVERT: C 284 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7656 (mtp) REVERT: G 176 LEU cc_start: 0.8643 (pp) cc_final: 0.8420 (mp) REVERT: G 187 TYR cc_start: 0.8765 (t80) cc_final: 0.8362 (t80) REVERT: G 222 ILE cc_start: 0.9070 (tp) cc_final: 0.8818 (tp) REVERT: G 224 ILE cc_start: 0.8319 (tp) cc_final: 0.8072 (tt) REVERT: G 270 ILE cc_start: 0.8822 (mm) cc_final: 0.8603 (mt) REVERT: H 94 GLU cc_start: 0.8193 (tp30) cc_final: 0.7898 (tm-30) REVERT: I 212 GLU cc_start: 0.8809 (tp30) cc_final: 0.8420 (tm-30) REVERT: I 246 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8379 (tm-30) outliers start: 37 outliers final: 22 residues processed: 233 average time/residue: 0.2221 time to fit residues: 76.7796 Evaluate side-chains 223 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 259 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.0060 chunk 129 optimal weight: 0.0060 chunk 39 optimal weight: 0.5980 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 177 ASN ** 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: 0.7902 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 : 0.002 0.032 12880 Z= 0.145 Angle : 0.577 13.106 17344 Z= 0.290 Chirality : 0.039 0.209 1907 Planarity : 0.003 0.055 2185 Dihedral : 4.733 33.700 1687 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.67 % Allowed : 20.25 % Favored : 77.08 % 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: -2.08 (0.21), residues: 1516 helix: -1.09 (0.15), residues: 1075 sheet: -3.07 (1.78), residues: 10 loop : -1.66 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 256 HIS 0.006 0.001 HIS E 304 PHE 0.026 0.001 PHE G 247 TYR 0.026 0.001 TYR A 410 ARG 0.006 0.000 ARG A 304 *********************** 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 250 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7149 (m-80) cc_final: 0.6667 (m-80) REVERT: A 183 MET cc_start: 0.8590 (ptm) cc_final: 0.8381 (ptm) REVERT: A 295 ASN cc_start: 0.8840 (t160) cc_final: 0.8520 (t0) REVERT: B 311 GLU cc_start: 0.7963 (tt0) cc_final: 0.7583 (tm-30) REVERT: B 384 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8270 (t80) REVERT: B 463 CYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6984 (t) REVERT: C 284 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: G 176 LEU cc_start: 0.8603 (pp) cc_final: 0.8393 (mp) REVERT: G 222 ILE cc_start: 0.9029 (tp) cc_final: 0.8726 (tp) REVERT: G 270 ILE cc_start: 0.8759 (mm) cc_final: 0.8556 (mt) REVERT: G 335 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.7659 (tpp-160) REVERT: H 94 GLU cc_start: 0.8272 (tp30) cc_final: 0.7862 (tm-30) REVERT: I 212 GLU cc_start: 0.8785 (tp30) cc_final: 0.8451 (tm-30) REVERT: I 246 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8245 (tm-30) REVERT: I 293 GLU cc_start: 0.8079 (mp0) cc_final: 0.7769 (mp0) REVERT: J 73 ILE cc_start: 0.8564 (tp) cc_final: 0.8177 (tt) outliers start: 36 outliers final: 20 residues processed: 230 average time/residue: 0.2188 time to fit residues: 76.0829 Evaluate side-chains 215 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 338 LEU 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: 2.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C 326 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12880 Z= 0.300 Angle : 0.636 12.017 17344 Z= 0.322 Chirality : 0.043 0.189 1907 Planarity : 0.004 0.051 2185 Dihedral : 4.916 36.971 1687 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.49 % Allowed : 21.44 % Favored : 75.07 % 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: -1.87 (0.21), residues: 1516 helix: -0.93 (0.16), residues: 1076 sheet: -3.00 (1.37), residues: 14 loop : -1.57 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.019 0.001 PHE G 247 TYR 0.021 0.001 TYR A 410 ARG 0.006 0.000 ARG J 52 *********************** 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 241 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 194 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7213 (m-80) cc_final: 0.6626 (m-80) REVERT: A 295 ASN cc_start: 0.8857 (t160) cc_final: 0.8548 (t0) REVERT: B 271 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7941 (mtmm) REVERT: B 311 GLU cc_start: 0.8028 (tt0) cc_final: 0.7676 (tm-30) REVERT: B 384 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8328 (t80) REVERT: B 413 CYS cc_start: 0.8466 (m) cc_final: 0.7972 (m) REVERT: B 463 CYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7183 (t) REVERT: G 176 LEU cc_start: 0.8719 (pp) cc_final: 0.8452 (mp) REVERT: G 222 ILE cc_start: 0.9064 (tp) cc_final: 0.8806 (tp) REVERT: G 243 MET cc_start: 0.8061 (ttm) cc_final: 0.7849 (mtp) REVERT: H 94 GLU cc_start: 0.8240 (tp30) cc_final: 0.7869 (tm-30) REVERT: I 212 GLU cc_start: 0.8862 (tp30) cc_final: 0.8561 (tm-30) REVERT: I 293 GLU cc_start: 0.8131 (mp0) cc_final: 0.7806 (mp0) REVERT: E 312 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6196 (p90) outliers start: 47 outliers final: 35 residues processed: 224 average time/residue: 0.2059 time to fit residues: 70.5511 Evaluate side-chains 227 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 0.7948 moved from start: 0.3314 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= 0.203 Angle : 0.604 12.122 17344 Z= 0.304 Chirality : 0.041 0.227 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.770 35.336 1687 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.19 % Allowed : 22.63 % Favored : 74.18 % 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: -1.56 (0.21), residues: 1516 helix: -0.68 (0.16), residues: 1083 sheet: -2.78 (1.38), residues: 14 loop : -1.54 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.016 0.001 PHE E 312 TYR 0.022 0.001 TYR G 187 ARG 0.005 0.000 ARG A 304 *********************** 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 241 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 198 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7188 (m-80) cc_final: 0.6609 (m-80) REVERT: A 183 MET cc_start: 0.8606 (ptm) cc_final: 0.8370 (ptm) REVERT: A 295 ASN cc_start: 0.8817 (t160) cc_final: 0.8522 (t0) REVERT: A 338 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: B 311 GLU cc_start: 0.7961 (tt0) cc_final: 0.7597 (tm-30) REVERT: B 384 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8163 (t80) REVERT: B 413 CYS cc_start: 0.8390 (m) cc_final: 0.7902 (m) REVERT: B 463 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7204 (t) REVERT: G 222 ILE cc_start: 0.9034 (tp) cc_final: 0.8780 (tp) REVERT: G 270 ILE cc_start: 0.8767 (mm) cc_final: 0.8526 (mt) REVERT: G 335 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.7585 (tpp-160) REVERT: H 94 GLU cc_start: 0.8364 (tp30) cc_final: 0.7915 (tm-30) REVERT: I 196 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: I 212 GLU cc_start: 0.8754 (tp30) cc_final: 0.8471 (tm-30) REVERT: I 246 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8288 (tm-30) REVERT: I 329 MET cc_start: 0.8513 (tmm) cc_final: 0.8275 (tmm) REVERT: E 312 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6433 (p90) REVERT: E 320 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7385 (tt) outliers start: 43 outliers final: 31 residues processed: 224 average time/residue: 0.2172 time to fit residues: 72.6467 Evaluate side-chains 226 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 I 177 ASN ** 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: 0.7945 moved from start: 0.3465 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= 0.199 Angle : 0.601 9.342 17344 Z= 0.303 Chirality : 0.041 0.221 1907 Planarity : 0.003 0.050 2185 Dihedral : 4.691 35.849 1687 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.19 % Allowed : 23.81 % Favored : 73.00 % 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: -1.34 (0.22), residues: 1516 helix: -0.49 (0.16), residues: 1089 sheet: -2.69 (1.39), residues: 14 loop : -1.56 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.020 0.001 PHE G 247 TYR 0.022 0.001 TYR G 187 ARG 0.007 0.000 ARG J 52 *********************** 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 234 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7195 (m-80) cc_final: 0.6621 (m-80) REVERT: A 183 MET cc_start: 0.8632 (ptm) cc_final: 0.8413 (ptm) REVERT: A 295 ASN cc_start: 0.8829 (t160) cc_final: 0.8537 (t0) REVERT: A 338 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8870 (m-80) REVERT: B 113 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: B 271 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7886 (mtmm) REVERT: B 311 GLU cc_start: 0.8009 (tt0) cc_final: 0.7713 (tm-30) REVERT: B 330 MET cc_start: 0.9527 (ttt) cc_final: 0.9112 (ttt) REVERT: B 384 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8187 (t80) REVERT: B 463 CYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7176 (t) REVERT: G 222 ILE cc_start: 0.9035 (tp) cc_final: 0.8789 (tp) REVERT: G 301 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8469 (mm) REVERT: G 335 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.7666 (tpp-160) REVERT: H 94 GLU cc_start: 0.8335 (tp30) cc_final: 0.7854 (tm-30) REVERT: I 196 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: I 212 GLU cc_start: 0.8763 (tp30) cc_final: 0.8520 (tm-30) REVERT: I 246 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8260 (tm-30) REVERT: J 73 ILE cc_start: 0.8633 (tp) cc_final: 0.8328 (tp) REVERT: E 312 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6511 (p90) REVERT: E 320 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7378 (tt) outliers start: 43 outliers final: 30 residues processed: 220 average time/residue: 0.2097 time to fit residues: 70.0684 Evaluate side-chains 225 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** 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** I 177 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3580 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= 0.187 Angle : 0.605 10.194 17344 Z= 0.304 Chirality : 0.041 0.226 1907 Planarity : 0.003 0.053 2185 Dihedral : 4.621 35.541 1687 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.26 % Allowed : 24.04 % Favored : 72.70 % 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: -1.15 (0.22), residues: 1516 helix: -0.35 (0.16), residues: 1092 sheet: -2.65 (1.39), residues: 14 loop : -1.48 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 255 HIS 0.005 0.001 HIS E 304 PHE 0.019 0.001 PHE G 247 TYR 0.013 0.001 TYR E 187 ARG 0.007 0.000 ARG F 52 *********************** 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 237 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7157 (m-80) cc_final: 0.6585 (m-80) REVERT: A 114 MET cc_start: 0.8053 (mtt) cc_final: 0.7692 (mtt) REVERT: A 183 MET cc_start: 0.8617 (ptm) cc_final: 0.8404 (ptm) REVERT: A 236 MET cc_start: 0.8674 (mtt) cc_final: 0.8031 (mmt) REVERT: A 295 ASN cc_start: 0.8911 (t0) cc_final: 0.8595 (t0) REVERT: A 338 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: B 113 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: B 271 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7879 (mtmm) REVERT: B 311 GLU cc_start: 0.8098 (tt0) cc_final: 0.7790 (tm-30) REVERT: B 330 MET cc_start: 0.9524 (ttt) cc_final: 0.9117 (ttt) REVERT: B 384 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.8110 (t80) REVERT: B 463 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7108 (t) REVERT: G 222 ILE cc_start: 0.8961 (tp) cc_final: 0.8676 (tp) REVERT: G 335 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7646 (tpp-160) REVERT: H 94 GLU cc_start: 0.8343 (tp30) cc_final: 0.7895 (tm-30) REVERT: I 196 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: I 212 GLU cc_start: 0.8689 (tp30) cc_final: 0.8476 (tm-30) REVERT: I 246 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8242 (tm-30) REVERT: I 293 GLU cc_start: 0.8002 (mp0) cc_final: 0.7696 (mp0) REVERT: J 73 ILE cc_start: 0.8507 (tp) cc_final: 0.8201 (tp) REVERT: E 320 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7368 (tt) outliers start: 44 outliers final: 33 residues processed: 222 average time/residue: 0.2214 time to fit residues: 74.2548 Evaluate side-chains 228 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 198 ASN I 177 ASN E 184 GLN E 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12880 Z= 0.179 Angle : 0.620 10.921 17344 Z= 0.308 Chirality : 0.040 0.251 1907 Planarity : 0.003 0.049 2185 Dihedral : 4.572 35.183 1687 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.56 % Allowed : 24.41 % Favored : 72.03 % 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: -0.96 (0.22), residues: 1516 helix: -0.20 (0.16), residues: 1089 sheet: -2.70 (1.36), residues: 14 loop : -1.42 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 255 HIS 0.004 0.001 HIS E 304 PHE 0.018 0.001 PHE G 247 TYR 0.020 0.001 TYR E 187 ARG 0.007 0.000 ARG J 52 *********************** 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 244 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 196 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7027 (m-80) cc_final: 0.6499 (m-80) REVERT: A 183 MET cc_start: 0.8611 (ptm) cc_final: 0.8400 (ptm) REVERT: A 236 MET cc_start: 0.8656 (mtt) cc_final: 0.8017 (mmt) REVERT: A 295 ASN cc_start: 0.8975 (t0) cc_final: 0.8663 (t0) REVERT: A 338 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: B 113 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: B 271 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7900 (mtmm) REVERT: B 311 GLU cc_start: 0.8102 (tt0) cc_final: 0.7801 (tm-30) REVERT: B 330 MET cc_start: 0.9535 (ttt) cc_final: 0.9158 (ttt) REVERT: B 384 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8144 (t80) REVERT: B 463 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7125 (t) REVERT: C 246 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 276 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6886 (mtt) REVERT: G 212 GLU cc_start: 0.8487 (pp20) cc_final: 0.8030 (pp20) REVERT: G 222 ILE cc_start: 0.8987 (tp) cc_final: 0.8731 (tp) REVERT: G 301 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8470 (mm) REVERT: H 94 GLU cc_start: 0.8322 (tp30) cc_final: 0.7856 (tm-30) REVERT: I 196 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: I 198 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8571 (m110) REVERT: I 246 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8139 (tm-30) REVERT: I 293 GLU cc_start: 0.7997 (mp0) cc_final: 0.7692 (mp0) REVERT: J 73 ILE cc_start: 0.8475 (tp) cc_final: 0.8179 (tp) REVERT: E 320 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7350 (tt) outliers start: 48 outliers final: 32 residues processed: 225 average time/residue: 0.2077 time to fit residues: 70.6786 Evaluate side-chains 231 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.277 Angle : 0.675 11.178 17344 Z= 0.340 Chirality : 0.043 0.258 1907 Planarity : 0.004 0.052 2185 Dihedral : 4.752 37.310 1687 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.12 % Allowed : 25.00 % Favored : 71.88 % 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: -0.23 (0.16), residues: 1089 sheet: -2.55 (1.45), residues: 14 loop : -1.47 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 255 HIS 0.004 0.001 HIS E 304 PHE 0.018 0.001 PHE G 247 TYR 0.015 0.001 TYR G 187 ARG 0.008 0.000 ARG J 52 ********************** 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 230 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 103 TYR cc_start: 0.7029 (m-80) cc_final: 0.6361 (m-80) REVERT: A 183 MET cc_start: 0.8628 (ptm) cc_final: 0.8389 (ptm) REVERT: A 236 MET cc_start: 0.8654 (mtt) cc_final: 0.8019 (mmt) REVERT: A 295 ASN cc_start: 0.9023 (t0) cc_final: 0.8699 (t0) REVERT: B 271 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7938 (mtmm) REVERT: B 311 GLU cc_start: 0.8142 (tt0) cc_final: 0.7834 (tm-30) REVERT: B 330 MET cc_start: 0.9511 (ttt) cc_final: 0.9105 (ttt) REVERT: B 384 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8140 (t80) REVERT: B 413 CYS cc_start: 0.8390 (m) cc_final: 0.7900 (m) REVERT: B 463 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7024 (t) REVERT: G 222 ILE cc_start: 0.9079 (tp) cc_final: 0.8826 (tp) REVERT: G 243 MET cc_start: 0.7673 (ttm) cc_final: 0.7439 (ttt) REVERT: G 301 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8414 (mm) REVERT: H 94 GLU cc_start: 0.8354 (tp30) cc_final: 0.7859 (tm-30) REVERT: I 196 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: I 293 GLU cc_start: 0.8022 (mp0) cc_final: 0.7709 (mp0) REVERT: J 73 ILE cc_start: 0.8738 (tp) cc_final: 0.8409 (tp) outliers start: 42 outliers final: 31 residues processed: 213 average time/residue: 0.2089 time to fit residues: 67.8246 Evaluate side-chains 220 residues out of total 1371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 196 GLN Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 312 PHE Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 71 PHE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 86 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.100773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071534 restraints weight = 30497.741| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.99 r_work: 0.3180 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12880 Z= 0.184 Angle : 0.667 13.362 17344 Z= 0.334 Chirality : 0.041 0.253 1907 Planarity : 0.003 0.050 2185 Dihedral : 4.657 35.386 1687 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.60 % Allowed : 25.59 % Favored : 71.81 % 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: -0.07 (0.16), residues: 1089 sheet: -2.67 (1.37), residues: 14 loop : -1.46 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 255 HIS 0.004 0.001 HIS E 304 PHE 0.017 0.001 PHE A 149 TYR 0.014 0.001 TYR G 187 ARG 0.008 0.000 ARG J 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2795.51 seconds wall clock time: 51 minutes 11.15 seconds (3071.15 seconds total)