Starting phenix.real_space_refine (version: dev) on Sun Feb 19 11:10:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/02_2023/6jmq_9849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/02_2023/6jmq_9849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/02_2023/6jmq_9849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/02_2023/6jmq_9849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/02_2023/6jmq_9849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmq_9849/02_2023/6jmq_9849_updated.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 219": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9950 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3101 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 383} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3520 Classifications: {'peptide': 451} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1526 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1593 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'CLR': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.00, per 1000 atoms: 0.60 Number of scatterers: 9950 At special positions: 0 Unit cell: (130.634, 83.979, 154.628, 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 35 16.00 O 1841 8.00 N 1606 7.00 C 6468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 210 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.02 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 200 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 704 " - " ASN B 424 " " NAG B 705 " - " ASN B 506 " " NAG B 706 " - " ASN B 365 " " NAG E 1 " - " ASN B 381 " Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 15 sheets defined 36.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.738A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.672A pdb=" N PHE A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR A 71 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Proline residue: A 72 - end of helix removed outlier: 3.632A pdb=" N VAL A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 76 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 77 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 112 removed outlier: 3.606A pdb=" N VAL A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 removed outlier: 4.110A pdb=" N TYR A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.513A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.940A pdb=" N LEU A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.793A pdb=" N ARG A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 245 through 253 removed outlier: 4.014A pdb=" N SER A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.535A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 4.029A pdb=" N VAL A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 311 through 318 removed outlier: 4.030A pdb=" N TYR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Proline residue: A 328 - end of helix No H-bonds generated for 'chain 'A' and resid 324 through 330' Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.593A pdb=" N ARG A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.529A pdb=" N THR A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 419 removed outlier: 3.618A pdb=" N ASN A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.812A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 4.020A pdb=" N ILE A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU A 469 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Proline residue: A 470 - end of helix removed outlier: 3.528A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 206 removed outlier: 4.224A pdb=" N LEU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.865A pdb=" N LYS B 245 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 249 " --> pdb=" O GLY B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.554A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.670A pdb=" N THR B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 removed outlier: 3.517A pdb=" N LEU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 447 through 459 removed outlier: 3.756A pdb=" N LEU B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG B 451 " --> pdb=" O GLN B 448 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 452 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 454 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 455 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 457 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.694A pdb=" N ASP B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 538 No H-bonds generated for 'chain 'B' and resid 535 through 538' Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.535A pdb=" N SER D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.616A pdb=" N GLU D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 189 through 193' Processing sheet with id= A, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.684A pdb=" N PHE B 466 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 377 through 379 removed outlier: 6.313A pdb=" N LEU B 399 " --> pdb=" O ALA B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.584A pdb=" N HIS B 556 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 542 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 597 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU B 595 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.778A pdb=" N GLN B 279 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 18 through 21 removed outlier: 3.586A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 92 through 95 removed outlier: 3.815A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 125 through 129 Processing sheet with id= H, first strand: chain 'C' and resid 156 through 159 removed outlier: 3.545A pdb=" N THR C 158 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 200 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 174 through 176 removed outlier: 3.633A pdb=" N VAL C 174 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= K, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.262A pdb=" N LYS D 109 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL D 13 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU D 111 " --> pdb=" O VAL D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 91 through 95 removed outlier: 3.600A pdb=" N TYR D 42 " --> pdb=" O TYR D 93 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK D 40 " --> pdb=" O UNK D 95 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN D 43 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.560A pdb=" N ASN D 143 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA D 136 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 138 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 182 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 168 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.873A pdb=" N TRP D 154 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 198 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 215 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 142 through 145 removed outlier: 5.500A pdb=" N TYR D 179 " --> pdb=" O ASN D 144 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 762 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: 2.83 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3056 1.34 - 1.46: 1941 1.46 - 1.57: 5149 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 10195 Sorted by residual: bond pdb=" C SER D 7 " pdb=" N PRO D 8 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.76e+01 bond pdb=" C GLU C 153 " pdb=" N PRO C 154 " ideal model delta sigma weight residual 1.333 1.369 -0.035 1.01e-02 9.80e+03 1.22e+01 bond pdb=" C1 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sigma weight residual 1.426 1.506 -0.080 3.20e-02 9.77e+02 6.30e+00 bond pdb=" C ARG A 427 " pdb=" N PRO A 428 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.34e+00 bond pdb=" C THR A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.25e-02 6.40e+03 3.35e+00 ... (remaining 10190 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.41: 329 106.41 - 113.49: 5772 113.49 - 120.58: 4142 120.58 - 127.66: 3568 127.66 - 134.75: 122 Bond angle restraints: 13933 Sorted by residual: angle pdb=" C UNK D 56 " pdb=" N UNK D 57 " pdb=" CA UNK D 57 " ideal model delta sigma weight residual 121.70 131.80 -10.10 1.80e+00 3.09e-01 3.15e+01 angle pdb=" N THR A 71 " pdb=" CA THR A 71 " pdb=" C THR A 71 " ideal model delta sigma weight residual 109.81 120.57 -10.76 2.21e+00 2.05e-01 2.37e+01 angle pdb=" C ILE D 156 " pdb=" N ASP D 157 " pdb=" CA ASP D 157 " ideal model delta sigma weight residual 122.46 128.46 -6.00 1.41e+00 5.03e-01 1.81e+01 angle pdb=" C SER A 126 " pdb=" N LEU A 127 " pdb=" CA LEU A 127 " ideal model delta sigma weight residual 120.06 125.12 -5.06 1.19e+00 7.06e-01 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" C LEU B 261 " ideal model delta sigma weight residual 110.35 116.09 -5.74 1.40e+00 5.10e-01 1.68e+01 ... (remaining 13928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.14: 5488 20.14 - 40.29: 411 40.29 - 60.43: 45 60.43 - 80.57: 10 80.57 - 100.72: 3 Dihedral angle restraints: 5957 sinusoidal: 2249 harmonic: 3708 Sorted by residual: dihedral pdb=" CA ARG A 427 " pdb=" C ARG A 427 " pdb=" N PRO A 428 " pdb=" CA PRO A 428 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C3 NAG B 704 " pdb=" C1 NAG B 704 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sinusoidal sigma weight residual -50.00 50.72 -100.72 1 2.00e+01 2.50e-03 2.85e+01 dihedral pdb=" CA ALA A 118 " pdb=" C ALA A 118 " pdb=" N TYR A 119 " pdb=" CA TYR A 119 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 5954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1225 0.051 - 0.102: 319 0.102 - 0.153: 91 0.153 - 0.204: 17 0.204 - 0.255: 4 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR A 71 " pdb=" N THR A 71 " pdb=" C THR A 71 " pdb=" CB THR A 71 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 424 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.56e+00 ... (remaining 1653 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 372 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 373 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 469 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 470 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 158 " -0.051 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO A 159 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.043 5.00e-02 4.00e+02 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2966 2.81 - 3.34: 8332 3.34 - 3.86: 15602 3.86 - 4.38: 17739 4.38 - 4.90: 30961 Nonbonded interactions: 75600 Sorted by model distance: nonbonded pdb=" OG SER B 535 " pdb=" O GLU B 561 " model vdw 2.293 2.440 nonbonded pdb=" O TYR B 250 " pdb=" OG SER B 253 " model vdw 2.298 2.440 nonbonded pdb=" NH2 ARG A 419 " pdb=" OE2 GLU A 426 " model vdw 2.358 2.520 nonbonded pdb=" O ILE A 139 " pdb=" OG SER A 143 " model vdw 2.361 2.440 nonbonded pdb=" O TRP B 363 " pdb=" OG1 THR B 367 " model vdw 2.372 2.440 ... (remaining 75595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 6468 2.51 5 N 1606 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.070 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: 0.000 Extract box with map and model: 5.540 Check model and map are aligned: 0.130 Process input model: 27.970 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.080 10195 Z= 0.322 Angle : 0.952 11.034 13933 Z= 0.524 Chirality : 0.052 0.255 1656 Planarity : 0.007 0.084 1716 Dihedral : 14.008 100.716 3555 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.57 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.18), residues: 1197 helix: -4.70 (0.09), residues: 437 sheet: -1.77 (0.34), residues: 211 loop : -2.77 (0.21), residues: 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 1.107 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.2265 time to fit residues: 66.4274 Evaluate side-chains 136 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 218 GLN A 293 ASN B 542 HIS B 560 ASN C 3 GLN D 6 GLN D 144 ASN D 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10195 Z= 0.230 Angle : 0.638 8.590 13933 Z= 0.320 Chirality : 0.042 0.313 1656 Planarity : 0.006 0.081 1716 Dihedral : 6.749 106.623 1435 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 1197 helix: -3.28 (0.17), residues: 440 sheet: -1.31 (0.33), residues: 229 loop : -2.37 (0.22), residues: 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.045 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 167 average time/residue: 0.2270 time to fit residues: 52.7344 Evaluate side-chains 151 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1083 time to fit residues: 4.6808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN B 556 HIS D 130 GLN D 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 10195 Z= 0.337 Angle : 0.684 8.537 13933 Z= 0.335 Chirality : 0.044 0.295 1656 Planarity : 0.005 0.080 1716 Dihedral : 6.718 107.177 1435 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer Outliers : 2.21 % 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: -3.13 (0.21), residues: 1197 helix: -2.43 (0.21), residues: 429 sheet: -1.05 (0.33), residues: 228 loop : -2.12 (0.23), residues: 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.108 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 143 average time/residue: 0.2284 time to fit residues: 46.4781 Evaluate side-chains 131 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0947 time to fit residues: 3.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10195 Z= 0.220 Angle : 0.613 9.605 13933 Z= 0.296 Chirality : 0.042 0.287 1656 Planarity : 0.005 0.078 1716 Dihedral : 6.434 107.041 1435 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 1.83 % 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: -2.62 (0.22), residues: 1197 helix: -1.81 (0.23), residues: 432 sheet: -0.94 (0.34), residues: 228 loop : -1.93 (0.24), residues: 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 146 average time/residue: 0.2232 time to fit residues: 45.9578 Evaluate side-chains 137 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0985 time to fit residues: 3.3985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 110 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10195 Z= 0.250 Angle : 0.618 8.536 13933 Z= 0.299 Chirality : 0.042 0.267 1656 Planarity : 0.005 0.079 1716 Dihedral : 6.404 107.418 1435 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 1.54 % 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: -2.30 (0.23), residues: 1197 helix: -1.43 (0.23), residues: 431 sheet: -0.87 (0.34), residues: 229 loop : -1.80 (0.25), residues: 537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 146 average time/residue: 0.2062 time to fit residues: 43.0101 Evaluate side-chains 137 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0886 time to fit residues: 2.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10195 Z= 0.207 Angle : 0.591 10.355 13933 Z= 0.284 Chirality : 0.041 0.258 1656 Planarity : 0.004 0.077 1716 Dihedral : 6.260 107.428 1435 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.15 % 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: -2.06 (0.23), residues: 1197 helix: -1.11 (0.24), residues: 428 sheet: -0.79 (0.35), residues: 222 loop : -1.73 (0.25), residues: 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.984 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 147 average time/residue: 0.2360 time to fit residues: 49.0707 Evaluate side-chains 132 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1013 time to fit residues: 2.5381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 122 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 220 HIS B 274 GLN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10195 Z= 0.172 Angle : 0.578 8.579 13933 Z= 0.278 Chirality : 0.040 0.246 1656 Planarity : 0.004 0.077 1716 Dihedral : 6.121 107.381 1435 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.23), residues: 1197 helix: -0.99 (0.24), residues: 444 sheet: -0.69 (0.35), residues: 220 loop : -1.71 (0.25), residues: 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.196 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 150 average time/residue: 0.2176 time to fit residues: 47.1258 Evaluate side-chains 132 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0917 time to fit residues: 2.6869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10195 Z= 0.262 Angle : 0.649 10.221 13933 Z= 0.312 Chirality : 0.042 0.243 1656 Planarity : 0.005 0.075 1716 Dihedral : 6.247 107.773 1435 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.23), residues: 1197 helix: -0.88 (0.24), residues: 447 sheet: -0.66 (0.34), residues: 224 loop : -1.71 (0.26), residues: 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.159 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 136 average time/residue: 0.2396 time to fit residues: 45.9910 Evaluate side-chains 132 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1106 time to fit residues: 2.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 0.0370 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 103 optimal weight: 0.0970 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 10195 Z= 0.156 Angle : 0.589 8.417 13933 Z= 0.280 Chirality : 0.040 0.241 1656 Planarity : 0.004 0.077 1716 Dihedral : 6.025 107.395 1435 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1197 helix: -0.57 (0.24), residues: 437 sheet: -0.52 (0.35), residues: 224 loop : -1.66 (0.26), residues: 536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.073 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 140 average time/residue: 0.2230 time to fit residues: 44.9319 Evaluate side-chains 126 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1009 time to fit residues: 2.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 116 optimal weight: 0.0040 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10195 Z= 0.190 Angle : 0.623 11.257 13933 Z= 0.293 Chirality : 0.041 0.228 1656 Planarity : 0.004 0.077 1716 Dihedral : 6.052 107.696 1435 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.19 % 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: -1.46 (0.24), residues: 1197 helix: -0.39 (0.25), residues: 431 sheet: -0.50 (0.35), residues: 220 loop : -1.59 (0.25), residues: 546 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.170 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 130 average time/residue: 0.2422 time to fit residues: 44.6039 Evaluate side-chains 127 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1397 time to fit residues: 2.0800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118483 restraints weight = 14656.069| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.33 r_work: 0.3243 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10195 Z= 0.245 Angle : 0.644 10.961 13933 Z= 0.305 Chirality : 0.042 0.232 1656 Planarity : 0.005 0.076 1716 Dihedral : 6.192 107.782 1435 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1197 helix: -0.40 (0.25), residues: 436 sheet: -0.55 (0.35), residues: 229 loop : -1.61 (0.26), residues: 532 =============================================================================== Job complete usr+sys time: 2321.41 seconds wall clock time: 43 minutes 1.14 seconds (2581.14 seconds total)