Starting phenix.real_space_refine on Thu Mar 14 22:59:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a92_11682/03_2024/7a92_11682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a92_11682/03_2024/7a92_11682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a92_11682/03_2024/7a92_11682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a92_11682/03_2024/7a92_11682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a92_11682/03_2024/7a92_11682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a92_11682/03_2024/7a92_11682.pdb" } resolution = 4.2 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 51 5.16 5 C 6424 2.51 5 N 1658 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D ASP 597": "OD1" <-> "OD2" Residue "D TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10040 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 bond proxies already assigned to first conformer: 4917 Chain: "A" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5098 Classifications: {'peptide': 643} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 609} Chain breaks: 2 Chain: "J" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.81, per 1000 atoms: 0.78 Number of scatterers: 10040 At special positions: 0 Unit cell: (89.474, 104.566, 168.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 51 16.00 O 1906 8.00 N 1658 7.00 C 6424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 343 " " NAG A 702 " - " ASN A 331 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG J 1 " - " ASN D 546 " Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 706 " pdb="ZN ZN D 706 " - pdb=" NE2 HIS D 374 " pdb="ZN ZN D 706 " - pdb=" NE2 HIS D 378 " 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 13 sheets defined 35.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.516A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 removed outlier: 3.537A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.794A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.866A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.528A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.701A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.603A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.508A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 3.815A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.125A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.909A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.574A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.853A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.552A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.718A pdb=" N TRP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.696A pdb=" N TRP D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.519A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.951A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.978A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.540A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.792A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 343' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.892A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.238A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.946A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.173A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.026A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.839A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.521A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.810A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.600A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.263A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1056 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: 2.84 Time building geometry restraints manager: 4.03 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: 3144 1.34 - 1.46: 2382 1.46 - 1.58: 4711 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 10311 Sorted by residual: bond pdb=" N LYS A 558 " pdb=" CA LYS A 558 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.27e-02 6.20e+03 1.16e+01 bond pdb=" CA SER A 591 " pdb=" CB SER A 591 " ideal model delta sigma weight residual 1.537 1.488 0.049 1.45e-02 4.76e+03 1.14e+01 bond pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.10e+01 bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL A 597 " pdb=" CA VAL A 597 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.75e+00 ... (remaining 10306 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.53: 214 105.53 - 112.69: 5218 112.69 - 119.85: 3629 119.85 - 127.01: 4819 127.01 - 134.17: 143 Bond angle restraints: 14023 Sorted by residual: angle pdb=" N VAL A 320 " pdb=" CA VAL A 320 " pdb=" C VAL A 320 " ideal model delta sigma weight residual 112.80 108.00 4.80 1.15e+00 7.56e-01 1.75e+01 angle pdb=" N PRO A 217 " pdb=" CA PRO A 217 " pdb=" C PRO A 217 " ideal model delta sigma weight residual 111.22 116.90 -5.68 1.40e+00 5.10e-01 1.64e+01 angle pdb=" C ASP A 578 " pdb=" CA ASP A 578 " pdb=" CB ASP A 578 " ideal model delta sigma weight residual 109.42 115.64 -6.22 1.57e+00 4.06e-01 1.57e+01 angle pdb=" CA ASN D 90 " pdb=" C ASN D 90 " pdb=" O ASN D 90 " ideal model delta sigma weight residual 120.55 116.40 4.15 1.06e+00 8.90e-01 1.54e+01 angle pdb=" CA ASN A 317 " pdb=" C ASN A 317 " pdb=" O ASN A 317 " ideal model delta sigma weight residual 121.87 117.65 4.22 1.16e+00 7.43e-01 1.32e+01 ... (remaining 14018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5591 17.99 - 35.98: 458 35.98 - 53.97: 121 53.97 - 71.97: 20 71.97 - 89.96: 12 Dihedral angle restraints: 6202 sinusoidal: 2593 harmonic: 3609 Sorted by residual: dihedral pdb=" CA SER D 425 " pdb=" C SER D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual 180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 131.58 -38.58 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA TYR D 252 " pdb=" C TYR D 252 " pdb=" N PRO D 253 " pdb=" CA PRO D 253 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 6199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1185 0.062 - 0.125: 303 0.125 - 0.187: 33 0.187 - 0.249: 7 0.249 - 0.311: 3 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CA ILE A 312 " pdb=" N ILE A 312 " pdb=" C ILE A 312 " pdb=" CB ILE A 312 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LEU A 216 " pdb=" N LEU A 216 " pdb=" C LEU A 216 " pdb=" CB LEU A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASP A 215 " pdb=" N ASP A 215 " pdb=" C ASP A 215 " pdb=" CB ASP A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1528 not shown) Planarity restraints: 1809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 451 " -0.016 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C PRO D 451 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO D 451 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE D 452 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 161 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C ARG D 161 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG D 161 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 162 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 368 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ASP D 368 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP D 368 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE D 369 " 0.013 2.00e-02 2.50e+03 ... (remaining 1806 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1623 2.76 - 3.29: 8995 3.29 - 3.83: 15235 3.83 - 4.36: 18612 4.36 - 4.90: 32588 Nonbonded interactions: 77053 Sorted by model distance: nonbonded pdb=" OG SER D 19 " pdb=" OE1 GLU D 23 " model vdw 2.222 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.227 2.440 nonbonded pdb=" O ASP D 225 " pdb=" OG1 THR D 229 " model vdw 2.230 2.440 nonbonded pdb=" O LEU D 85 " pdb=" NZ LYS D 94 " model vdw 2.269 2.520 nonbonded pdb=" OH TYR D 41 " pdb=" OG1 THR A 500 " model vdw 2.272 2.440 ... (remaining 77048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 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: 13.150 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 33.620 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 : 0.007 0.060 10311 Z= 0.436 Angle : 0.844 9.732 14023 Z= 0.484 Chirality : 0.056 0.311 1531 Planarity : 0.006 0.054 1801 Dihedral : 14.642 89.957 3847 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 1.19 % Allowed : 4.87 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -2.44 (0.22), residues: 1223 helix: -1.66 (0.24), residues: 387 sheet: -0.12 (0.34), residues: 214 loop : -2.15 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 594 HIS 0.007 0.002 HIS D 265 PHE 0.024 0.003 PHE A 543 TYR 0.018 0.002 TYR A 421 ARG 0.010 0.001 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 ASP cc_start: 0.8324 (t0) cc_final: 0.7850 (p0) REVERT: A 322 PRO cc_start: 0.5932 (Cg_exo) cc_final: 0.5656 (Cg_endo) outliers start: 13 outliers final: 2 residues processed: 147 average time/residue: 0.1994 time to fit residues: 42.1837 Evaluate side-chains 64 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 110 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 287 GLN D 325 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 115 GLN A 164 ASN A 218 GLN A 239 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 580 GLN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10311 Z= 0.187 Angle : 0.613 11.715 14023 Z= 0.321 Chirality : 0.044 0.220 1531 Planarity : 0.004 0.047 1801 Dihedral : 6.870 56.172 1526 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.50 (0.23), residues: 1223 helix: -0.21 (0.26), residues: 386 sheet: 0.01 (0.34), residues: 213 loop : -1.90 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 152 HIS 0.003 0.001 HIS D 535 PHE 0.012 0.001 PHE A 643 TYR 0.018 0.001 TYR D 199 ARG 0.005 0.001 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.6262 (p0) cc_final: 0.6020 (p0) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.1805 time to fit residues: 20.8038 Evaluate side-chains 45 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 0.0060 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 ASN D 96 GLN D 552 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10311 Z= 0.160 Angle : 0.544 6.817 14023 Z= 0.283 Chirality : 0.043 0.206 1531 Planarity : 0.004 0.046 1801 Dihedral : 6.347 56.330 1526 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.88 (0.23), residues: 1223 helix: 0.53 (0.27), residues: 379 sheet: 0.23 (0.35), residues: 215 loop : -1.63 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS D 535 PHE 0.021 0.001 PHE A 374 TYR 0.013 0.001 TYR A 612 ARG 0.003 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.8232 (ttp) cc_final: 0.7898 (ttp) REVERT: D 579 MET cc_start: 0.8173 (pmm) cc_final: 0.7969 (ptp) REVERT: A 177 MET cc_start: 0.3872 (mmp) cc_final: 0.2997 (mtp) REVERT: A 428 ASP cc_start: 0.6290 (p0) cc_final: 0.6024 (p0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1854 time to fit residues: 21.5534 Evaluate side-chains 47 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 0.0870 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 GLN A 146 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10311 Z= 0.284 Angle : 0.652 7.678 14023 Z= 0.338 Chirality : 0.044 0.195 1531 Planarity : 0.004 0.041 1801 Dihedral : 6.190 57.381 1526 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.79 (0.23), residues: 1223 helix: 0.59 (0.27), residues: 376 sheet: 0.38 (0.38), residues: 185 loop : -1.50 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 271 HIS 0.011 0.002 HIS D 378 PHE 0.016 0.002 PHE D 390 TYR 0.036 0.002 TYR A 396 ARG 0.006 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.8206 (ttp) cc_final: 0.7788 (ttp) REVERT: D 123 MET cc_start: 0.7488 (mtp) cc_final: 0.7134 (mtt) REVERT: A 428 ASP cc_start: 0.6428 (p0) cc_final: 0.6158 (p0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1896 time to fit residues: 17.2550 Evaluate side-chains 41 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 39 optimal weight: 0.0040 overall best weight: 0.1870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 501 ASN A 641 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10311 Z= 0.131 Angle : 0.533 9.200 14023 Z= 0.273 Chirality : 0.043 0.198 1531 Planarity : 0.003 0.043 1801 Dihedral : 5.803 56.635 1526 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.51 (0.24), residues: 1223 helix: 0.83 (0.27), residues: 385 sheet: 0.53 (0.37), residues: 209 loop : -1.44 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 302 HIS 0.003 0.001 HIS D 535 PHE 0.012 0.001 PHE D 315 TYR 0.019 0.001 TYR A 396 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: D 123 MET cc_start: 0.7393 (mtp) cc_final: 0.7190 (mtt) REVERT: D 366 MET cc_start: 0.6058 (mtp) cc_final: 0.5303 (ttm) REVERT: D 557 MET cc_start: 0.8381 (tmm) cc_final: 0.8154 (tmm) REVERT: A 428 ASP cc_start: 0.6563 (p0) cc_final: 0.6291 (p0) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2053 time to fit residues: 17.8350 Evaluate side-chains 44 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10311 Z= 0.179 Angle : 0.540 7.784 14023 Z= 0.277 Chirality : 0.043 0.201 1531 Planarity : 0.003 0.041 1801 Dihedral : 5.704 56.150 1526 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.42 (0.24), residues: 1223 helix: 0.94 (0.27), residues: 386 sheet: 0.56 (0.37), residues: 210 loop : -1.40 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 302 HIS 0.006 0.001 HIS D 378 PHE 0.013 0.001 PHE A 168 TYR 0.021 0.001 TYR A 396 ARG 0.002 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.7533 (mtp) cc_final: 0.7245 (mtt) REVERT: D 366 MET cc_start: 0.6112 (mtp) cc_final: 0.5361 (ttm) REVERT: D 557 MET cc_start: 0.8451 (tmm) cc_final: 0.8170 (tmm) REVERT: A 428 ASP cc_start: 0.6487 (p0) cc_final: 0.6220 (p0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1884 time to fit residues: 15.9224 Evaluate side-chains 40 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 0.0060 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10311 Z= 0.158 Angle : 0.529 7.643 14023 Z= 0.269 Chirality : 0.042 0.192 1531 Planarity : 0.003 0.043 1801 Dihedral : 5.546 55.968 1526 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.31 (0.24), residues: 1223 helix: 1.03 (0.27), residues: 391 sheet: 0.47 (0.36), residues: 220 loop : -1.31 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 302 HIS 0.005 0.001 HIS D 378 PHE 0.019 0.001 PHE D 327 TYR 0.019 0.001 TYR A 396 ARG 0.002 0.000 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.7489 (mtp) cc_final: 0.7206 (mtt) REVERT: D 366 MET cc_start: 0.6068 (mtp) cc_final: 0.5238 (ttm) REVERT: D 557 MET cc_start: 0.8477 (tmm) cc_final: 0.8195 (tmm) REVERT: A 428 ASP cc_start: 0.6438 (p0) cc_final: 0.6131 (p0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1820 time to fit residues: 16.7843 Evaluate side-chains 40 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10311 Z= 0.168 Angle : 0.526 7.219 14023 Z= 0.268 Chirality : 0.042 0.189 1531 Planarity : 0.003 0.040 1801 Dihedral : 5.459 55.889 1526 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.20 (0.24), residues: 1223 helix: 1.06 (0.27), residues: 391 sheet: 0.58 (0.35), residues: 224 loop : -1.24 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 302 HIS 0.008 0.001 HIS D 535 PHE 0.014 0.001 PHE D 428 TYR 0.019 0.001 TYR A 396 ARG 0.002 0.000 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.7507 (mtp) cc_final: 0.7272 (mtt) REVERT: D 366 MET cc_start: 0.6153 (mtp) cc_final: 0.5325 (ttm) REVERT: D 376 MET cc_start: 0.8266 (tpp) cc_final: 0.8001 (tpp) REVERT: D 557 MET cc_start: 0.8492 (tmm) cc_final: 0.8151 (tmm) REVERT: A 428 ASP cc_start: 0.6465 (p0) cc_final: 0.6156 (p0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1877 time to fit residues: 15.8477 Evaluate side-chains 40 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS A ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10311 Z= 0.174 Angle : 0.532 10.846 14023 Z= 0.272 Chirality : 0.043 0.201 1531 Planarity : 0.003 0.042 1801 Dihedral : 5.463 55.937 1526 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.21 (0.24), residues: 1223 helix: 1.05 (0.27), residues: 391 sheet: 0.59 (0.38), residues: 196 loop : -1.16 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 302 HIS 0.005 0.001 HIS D 378 PHE 0.014 0.001 PHE D 428 TYR 0.019 0.001 TYR A 396 ARG 0.002 0.000 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.7493 (mtp) cc_final: 0.7274 (mtt) REVERT: D 366 MET cc_start: 0.6191 (mtp) cc_final: 0.5383 (ttm) REVERT: D 376 MET cc_start: 0.8259 (tpp) cc_final: 0.7860 (tpp) REVERT: D 557 MET cc_start: 0.8491 (tmm) cc_final: 0.8162 (tmm) REVERT: A 428 ASP cc_start: 0.6534 (p0) cc_final: 0.6249 (p0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1957 time to fit residues: 17.0557 Evaluate side-chains 38 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 0.0020 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10311 Z= 0.172 Angle : 0.530 7.098 14023 Z= 0.272 Chirality : 0.043 0.194 1531 Planarity : 0.004 0.042 1801 Dihedral : 5.428 55.832 1526 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.14 (0.24), residues: 1223 helix: 1.10 (0.27), residues: 393 sheet: 0.65 (0.39), residues: 189 loop : -1.11 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 473 HIS 0.005 0.001 HIS D 378 PHE 0.015 0.001 PHE D 428 TYR 0.018 0.001 TYR A 396 ARG 0.004 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.7506 (mtp) cc_final: 0.7213 (mtt) REVERT: D 366 MET cc_start: 0.6156 (mtp) cc_final: 0.5401 (ttm) REVERT: D 376 MET cc_start: 0.8123 (tpp) cc_final: 0.7820 (tpp) REVERT: D 455 MET cc_start: 0.8218 (ppp) cc_final: 0.7974 (ppp) REVERT: D 557 MET cc_start: 0.8461 (tmm) cc_final: 0.8105 (tmm) REVERT: A 428 ASP cc_start: 0.6563 (p0) cc_final: 0.6273 (p0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1741 time to fit residues: 16.4134 Evaluate side-chains 37 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.069401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.042854 restraints weight = 113564.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045346 restraints weight = 45365.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046927 restraints weight = 26664.047| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10311 Z= 0.185 Angle : 0.536 7.922 14023 Z= 0.275 Chirality : 0.043 0.192 1531 Planarity : 0.004 0.043 1801 Dihedral : 5.429 56.000 1526 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1223 helix: 1.08 (0.27), residues: 393 sheet: 0.58 (0.38), residues: 196 loop : -1.10 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 302 HIS 0.005 0.001 HIS D 378 PHE 0.017 0.001 PHE D 512 TYR 0.018 0.001 TYR A 396 ARG 0.002 0.000 ARG D 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.60 seconds wall clock time: 38 minutes 55.55 seconds (2335.55 seconds total)