Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 09:26:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or2_17115/10_2023/8or2_17115.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or2_17115/10_2023/8or2_17115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or2_17115/10_2023/8or2_17115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or2_17115/10_2023/8or2_17115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or2_17115/10_2023/8or2_17115.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or2_17115/10_2023/8or2_17115.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 3 6.06 5 S 99 5.16 5 C 10554 2.51 5 N 2816 2.21 5 O 3086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 675": "OD1" <-> "OD2" Residue "C ARG 829": "NH1" <-> "NH2" Residue "C GLU 856": "OE1" <-> "OE2" Residue "C TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 898": "OE1" <-> "OE2" Residue "C TYR 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 915": "OE1" <-> "OE2" Residue "C TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1017": "OD1" <-> "OD2" Residue "C PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C GLU 1061": "OE1" <-> "OE2" Residue "C TYR 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1167": "OE1" <-> "OE2" Residue "C GLU 1171": "OE1" <-> "OE2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F ASP 211": "OD1" <-> "OD2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F GLU 233": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 16558 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5651 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 677} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 8808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8808 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 7 Chain: "F" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1365 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5876 SG CYS B 45 126.042 64.210 43.049 1.00 56.54 S ATOM 6171 SG CYS B 83 125.084 62.262 46.086 1.00 54.48 S ATOM 6100 SG CYS B 75 126.480 75.706 52.362 1.00 53.89 S ATOM 6267 SG CYS B 94 129.544 72.330 52.823 1.00 53.87 S ATOM 5943 SG CYS B 53 121.363 59.522 43.325 1.00 58.28 S ATOM 5966 SG CYS B 56 118.661 58.356 43.069 1.00 60.30 S ATOM 6050 SG CYS B 68 117.351 61.442 42.096 1.00 55.90 S Time building chain proxies: 9.17, per 1000 atoms: 0.55 Number of scatterers: 16558 At special positions: 0 Unit cell: (150.12, 133.92, 166.32, 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 3 29.99 S 99 16.00 O 3086 8.00 N 2816 7.00 C 10554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B4001 " pdb="ZN ZN B4001 " - pdb=" ND1 HIS B 80 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 45 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 83 " pdb=" ZN B4002 " pdb="ZN ZN B4002 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 94 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 75 " pdb=" ZN B4003 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 56 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 68 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 53 " 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3998 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 5 sheets defined 73.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.953A pdb=" N GLN A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.531A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.756A pdb=" N ARG A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 191 removed outlier: 3.597A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 4.032A pdb=" N ILE A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.536A pdb=" N PHE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.786A pdb=" N GLN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 279 removed outlier: 3.600A pdb=" N TYR A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.378A pdb=" N GLU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.564A pdb=" N GLU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.910A pdb=" N ARG A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 355 removed outlier: 3.643A pdb=" N CYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.900A pdb=" N ALA A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.861A pdb=" N LEU A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.706A pdb=" N GLU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 525 Processing helix chain 'A' and resid 559 through 572 removed outlier: 3.604A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 690 through 722 removed outlier: 3.790A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.677A pdb=" N LEU A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 759 removed outlier: 3.776A pdb=" N LYS A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.852A pdb=" N ASN B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.968A pdb=" N ASN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.518A pdb=" N ARG C 23 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 36 Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 61 through 78 removed outlier: 3.893A pdb=" N GLY C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.742A pdb=" N SER C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 78 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.674A pdb=" N VAL C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 128 through 142 Processing helix chain 'C' and resid 148 through 165 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.860A pdb=" N MET C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 4.431A pdb=" N GLU C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 249 through 253 removed outlier: 4.050A pdb=" N LEU C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 270 through 285 removed outlier: 4.333A pdb=" N TYR C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 3.556A pdb=" N VAL C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 removed outlier: 3.806A pdb=" N ARG C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL C 360 " --> pdb=" O CYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 375 through 383 Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.633A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 443 removed outlier: 3.639A pdb=" N GLN C 431 " --> pdb=" O MET C 427 " (cutoff:3.500A) Proline residue: C 433 - end of helix removed outlier: 3.870A pdb=" N LYS C 437 " --> pdb=" O PRO C 433 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 441 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 465 Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'C' and resid 508 through 515 removed outlier: 6.121A pdb=" N GLN C 511 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N HIS C 514 " --> pdb=" O GLN C 511 " (cutoff:3.500A) Proline residue: C 515 - end of helix Processing helix chain 'C' and resid 516 through 529 Proline residue: C 522 - end of helix removed outlier: 3.548A pdb=" N GLY C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.518A pdb=" N LYS C 548 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 564 through 577 removed outlier: 4.197A pdb=" N ARG C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 606 through 621 removed outlier: 4.700A pdb=" N ASN C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 617 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 651 through 657 Processing helix chain 'C' and resid 658 through 660 No H-bonds generated for 'chain 'C' and resid 658 through 660' Processing helix chain 'C' and resid 663 through 681 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.768A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 766 removed outlier: 3.829A pdb=" N SER C 753 " --> pdb=" O GLY C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 780 Processing helix chain 'C' and resid 792 through 810 Processing helix chain 'C' and resid 813 through 826 removed outlier: 3.858A pdb=" N VAL C 817 " --> pdb=" O GLU C 813 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 818 " --> pdb=" O GLY C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 846 Processing helix chain 'C' and resid 856 through 866 removed outlier: 3.588A pdb=" N VAL C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 866 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 887 removed outlier: 3.603A pdb=" N VAL C 885 " --> pdb=" O GLY C 881 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY C 886 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 887 " --> pdb=" O ILE C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 Proline residue: C 893 - end of helix removed outlier: 3.725A pdb=" N THR C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 920 removed outlier: 3.873A pdb=" N HIS C 911 " --> pdb=" O TYR C 907 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 918 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 929 through 941 removed outlier: 4.365A pdb=" N GLU C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 959 Processing helix chain 'C' and resid 962 through 977 Proline residue: C 968 - end of helix removed outlier: 3.511A pdb=" N LEU C 974 " --> pdb=" O LEU C 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 975 " --> pdb=" O LYS C 971 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 991 removed outlier: 3.871A pdb=" N PHE C 991 " --> pdb=" O THR C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1014 removed outlier: 4.248A pdb=" N GLY C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP C1010 " --> pdb=" O ASN C1006 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C1011 " --> pdb=" O CYS C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1037 Processing helix chain 'C' and resid 1044 through 1057 Proline residue: C1050 - end of helix removed outlier: 3.938A pdb=" N LYS C1057 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1092 removed outlier: 3.662A pdb=" N ARG C1082 " --> pdb=" O GLY C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1113 removed outlier: 3.620A pdb=" N ASN C1107 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N HIS C1108 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C1109 " --> pdb=" O PHE C1105 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1131 Processing helix chain 'C' and resid 1134 through 1140 removed outlier: 3.600A pdb=" N VAL C1138 " --> pdb=" O CYS C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1154 Proline residue: C1148 - end of helix Processing helix chain 'C' and resid 1162 through 1185 removed outlier: 3.596A pdb=" N PHE C1166 " --> pdb=" O VAL C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1201 through 1204 Processing helix chain 'C' and resid 1205 through 1210 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 99 through 109 removed outlier: 4.161A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 109 " --> pdb=" O ILE F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 Proline residue: F 142 - end of helix removed outlier: 3.859A pdb=" N GLU F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 166 removed outlier: 3.822A pdb=" N ASP F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN F 163 " --> pdb=" O GLN F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 removed outlier: 3.548A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 199 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.709A pdb=" N TRP F 213 " --> pdb=" O PRO F 209 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU F 217 " --> pdb=" O TRP F 213 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP F 218 " --> pdb=" O ASN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 251 Proline residue: F 249 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 541 removed outlier: 6.686A pdb=" N SER A 536 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 31 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP B 33 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 540 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N TRP B 35 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL B 24 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N GLY A 588 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 12.651A pdb=" N LYS B 26 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N SER A 586 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ASN B 28 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLN A 584 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 30 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 600 " --> pdb=" O VAL A 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 726 Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.691A pdb=" N ARG B 99 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1063 through 1066 removed outlier: 3.727A pdb=" N VAL C1066 " --> pdb=" O HIS C1073 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS C1073 " --> pdb=" O VAL C1066 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2862 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: 5.26 Time building geometry restraints manager: 7.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2763 1.28 - 1.41: 3876 1.41 - 1.54: 10033 1.54 - 1.68: 15 1.68 - 1.81: 148 Bond restraints: 16835 Sorted by residual: bond pdb=" C VAL A 724 " pdb=" O VAL A 724 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.19e-02 7.06e+03 5.91e+01 bond pdb=" CA ILE A 755 " pdb=" C ILE A 755 " ideal model delta sigma weight residual 1.524 1.425 0.099 1.30e-02 5.92e+03 5.77e+01 bond pdb=" C ARG B 91 " pdb=" N GLN B 92 " ideal model delta sigma weight residual 1.333 1.450 -0.117 1.55e-02 4.16e+03 5.69e+01 bond pdb=" C LYS A 720 " pdb=" O LYS A 720 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.19e-02 7.06e+03 4.98e+01 bond pdb=" C PRO F 209 " pdb=" O PRO F 209 " ideal model delta sigma weight residual 1.233 1.151 0.082 1.18e-02 7.18e+03 4.87e+01 ... (remaining 16830 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.23: 262 105.23 - 112.42: 8724 112.42 - 119.61: 5624 119.61 - 126.81: 7938 126.81 - 134.00: 183 Bond angle restraints: 22731 Sorted by residual: angle pdb=" N ALA F 235 " pdb=" CA ALA F 235 " pdb=" C ALA F 235 " ideal model delta sigma weight residual 113.01 125.11 -12.10 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N VAL A 658 " pdb=" CA VAL A 658 " pdb=" C VAL A 658 " ideal model delta sigma weight residual 110.72 120.81 -10.09 1.01e+00 9.80e-01 9.99e+01 angle pdb=" N VAL F 238 " pdb=" CA VAL F 238 " pdb=" C VAL F 238 " ideal model delta sigma weight residual 112.98 125.45 -12.47 1.25e+00 6.40e-01 9.95e+01 angle pdb=" N SER C 17 " pdb=" CA SER C 17 " pdb=" C SER C 17 " ideal model delta sigma weight residual 112.54 124.11 -11.57 1.22e+00 6.72e-01 8.99e+01 angle pdb=" O GLN B 92 " pdb=" C GLN B 92 " pdb=" N VAL B 93 " ideal model delta sigma weight residual 122.46 109.60 12.86 1.37e+00 5.33e-01 8.82e+01 ... (remaining 22726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9213 17.99 - 35.98: 952 35.98 - 53.97: 158 53.97 - 71.96: 26 71.96 - 89.95: 14 Dihedral angle restraints: 10363 sinusoidal: 4245 harmonic: 6118 Sorted by residual: dihedral pdb=" N TYR A 772 " pdb=" C TYR A 772 " pdb=" CA TYR A 772 " pdb=" CB TYR A 772 " ideal model delta harmonic sigma weight residual 122.80 107.11 15.69 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C VAL F 238 " pdb=" N VAL F 238 " pdb=" CA VAL F 238 " pdb=" CB VAL F 238 " ideal model delta harmonic sigma weight residual -122.00 -137.16 15.16 0 2.50e+00 1.60e-01 3.68e+01 dihedral pdb=" N VAL F 238 " pdb=" C VAL F 238 " pdb=" CA VAL F 238 " pdb=" CB VAL F 238 " ideal model delta harmonic sigma weight residual 123.40 138.07 -14.67 0 2.50e+00 1.60e-01 3.45e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2583 0.139 - 0.278: 34 0.278 - 0.418: 13 0.418 - 0.557: 5 0.557 - 0.696: 6 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CA ALA F 235 " pdb=" N ALA F 235 " pdb=" C ALA F 235 " pdb=" CB ALA F 235 " both_signs ideal model delta sigma weight residual False 2.48 1.79 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA VAL F 238 " pdb=" N VAL F 238 " pdb=" C VAL F 238 " pdb=" CB VAL F 238 " both_signs ideal model delta sigma weight residual False 2.44 1.77 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA THR F 212 " pdb=" N THR F 212 " pdb=" C THR F 212 " pdb=" CB THR F 212 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2638 not shown) Planarity restraints: 2869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 772 " 0.075 2.00e-02 2.50e+03 3.81e-02 2.91e+01 pdb=" CG TYR A 772 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 772 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 772 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 772 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 772 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 772 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 772 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 681 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ARG A 681 " 0.084 2.00e-02 2.50e+03 pdb=" O ARG A 681 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL A 682 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1060 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LYS C1060 " 0.083 2.00e-02 2.50e+03 pdb=" O LYS C1060 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU C1061 " -0.028 2.00e-02 2.50e+03 ... (remaining 2866 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 52 2.42 - 3.04: 11075 3.04 - 3.66: 24143 3.66 - 4.28: 33845 4.28 - 4.90: 57547 Nonbonded interactions: 126662 Sorted by model distance: nonbonded pdb=" CB HIS A 727 " pdb=" OD1 ASP A 770 " model vdw 1.805 3.440 nonbonded pdb=" O ILE C 654 " pdb=" OG SER C 657 " model vdw 2.105 2.440 nonbonded pdb=" O PRO C 893 " pdb=" NE2 GLN C 897 " model vdw 2.125 2.520 nonbonded pdb=" O GLN A 463 " pdb=" OH TYR A 500 " model vdw 2.137 2.440 nonbonded pdb=" O THR C 624 " pdb=" OG1 THR C 628 " model vdw 2.139 2.440 ... (remaining 126657 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.020 Extract box with map and model: 7.600 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 46.830 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 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 0.127 16835 Z= 0.458 Angle : 0.761 12.916 22731 Z= 0.486 Chirality : 0.058 0.696 2641 Planarity : 0.004 0.049 2869 Dihedral : 14.647 89.947 6365 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.24 % Allowed : 1.50 % Favored : 97.26 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 2032 helix: 2.50 (0.15), residues: 1388 sheet: -1.91 (1.31), residues: 12 loop : -1.45 (0.25), residues: 632 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 341 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 359 average time/residue: 0.2961 time to fit residues: 158.0169 Evaluate side-chains 333 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 320 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1522 time to fit residues: 6.4230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 518 ASN A 657 ASN C 151 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS C 848 HIS ** C1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16835 Z= 0.275 Angle : 0.637 10.737 22731 Z= 0.323 Chirality : 0.041 0.152 2641 Planarity : 0.005 0.067 2869 Dihedral : 3.370 22.343 2219 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.34 % Allowed : 8.92 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 2032 helix: 1.83 (0.14), residues: 1412 sheet: -1.69 (1.15), residues: 12 loop : -1.65 (0.24), residues: 608 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 351 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 358 average time/residue: 0.3067 time to fit residues: 161.4792 Evaluate side-chains 341 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 326 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1990 time to fit residues: 7.7799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 63 optimal weight: 0.4980 chunk 149 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 518 ASN A 712 GLN C 511 GLN C 603 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS C1164 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16835 Z= 0.198 Angle : 0.560 13.038 22731 Z= 0.279 Chirality : 0.038 0.156 2641 Planarity : 0.004 0.047 2869 Dihedral : 3.264 23.075 2219 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.34 % Allowed : 12.78 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 2032 helix: 1.84 (0.14), residues: 1420 sheet: -1.79 (1.12), residues: 12 loop : -1.73 (0.23), residues: 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 340 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 351 average time/residue: 0.3048 time to fit residues: 156.9895 Evaluate side-chains 337 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 321 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1858 time to fit residues: 8.2082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.0670 chunk 140 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 0.0770 chunk 187 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 177 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN C 404 GLN C 610 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16835 Z= 0.152 Angle : 0.550 13.174 22731 Z= 0.271 Chirality : 0.036 0.159 2641 Planarity : 0.004 0.045 2869 Dihedral : 3.218 22.184 2219 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.50 % Allowed : 14.72 % Favored : 83.78 % 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: 1.30 (0.19), residues: 2032 helix: 1.90 (0.14), residues: 1423 sheet: -1.78 (1.17), residues: 12 loop : -1.75 (0.23), residues: 597 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 321 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 339 average time/residue: 0.3067 time to fit residues: 153.8613 Evaluate side-chains 327 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 315 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1677 time to fit residues: 6.7120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.2980 chunk 112 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN C 662 ASN C 748 GLN C 847 HIS C 854 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16835 Z= 0.179 Angle : 0.557 13.696 22731 Z= 0.276 Chirality : 0.037 0.184 2641 Planarity : 0.004 0.046 2869 Dihedral : 3.259 23.687 2219 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.45 % Allowed : 15.15 % Favored : 83.40 % 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: 1.22 (0.19), residues: 2032 helix: 1.80 (0.14), residues: 1429 sheet: -1.69 (1.15), residues: 12 loop : -1.68 (0.23), residues: 591 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 328 time to evaluate : 1.926 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 341 average time/residue: 0.3200 time to fit residues: 159.6206 Evaluate side-chains 331 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 318 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1790 time to fit residues: 6.6099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.2980 chunk 178 optimal weight: 0.0970 chunk 39 optimal weight: 0.0060 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 65 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN C 610 ASN C 847 HIS F 163 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16835 Z= 0.147 Angle : 0.551 14.008 22731 Z= 0.271 Chirality : 0.036 0.170 2641 Planarity : 0.004 0.046 2869 Dihedral : 3.205 23.049 2219 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.07 % Allowed : 16.60 % Favored : 82.33 % 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: 1.37 (0.19), residues: 2032 helix: 1.91 (0.14), residues: 1429 sheet: -1.72 (1.20), residues: 12 loop : -1.63 (0.23), residues: 591 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 327 time to evaluate : 1.875 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 338 average time/residue: 0.3318 time to fit residues: 161.8232 Evaluate side-chains 323 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 317 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2175 time to fit residues: 4.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 112 optimal weight: 0.0050 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN A 696 GLN C 429 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16835 Z= 0.191 Angle : 0.575 13.692 22731 Z= 0.284 Chirality : 0.038 0.162 2641 Planarity : 0.004 0.046 2869 Dihedral : 3.313 24.407 2219 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.61 % Allowed : 17.19 % Favored : 81.20 % 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: 1.24 (0.19), residues: 2032 helix: 1.80 (0.14), residues: 1429 sheet: -1.72 (1.18), residues: 12 loop : -1.62 (0.23), residues: 591 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 318 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 331 average time/residue: 0.3408 time to fit residues: 162.6779 Evaluate side-chains 330 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 314 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1928 time to fit residues: 8.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 0.0060 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 155 optimal weight: 0.0010 chunk 179 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 518 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1073 HIS ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16835 Z= 0.170 Angle : 0.583 14.229 22731 Z= 0.286 Chirality : 0.037 0.163 2641 Planarity : 0.004 0.045 2869 Dihedral : 3.312 24.089 2219 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.59 % Allowed : 17.94 % Favored : 81.47 % 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: 1.30 (0.19), residues: 2032 helix: 1.84 (0.14), residues: 1433 sheet: -1.81 (1.20), residues: 12 loop : -1.61 (0.23), residues: 587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 315 time to evaluate : 2.043 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 320 average time/residue: 0.3213 time to fit residues: 149.1761 Evaluate side-chains 311 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 305 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1654 time to fit residues: 4.4231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8563 > 50: distance: 18 - 36: 25.730 distance: 22 - 40: 25.009 distance: 32 - 36: 28.302 distance: 36 - 37: 5.719 distance: 37 - 38: 10.660 distance: 38 - 39: 24.628 distance: 38 - 40: 32.381 distance: 40 - 41: 37.379 distance: 41 - 42: 5.775 distance: 41 - 44: 26.909 distance: 42 - 43: 6.895 distance: 42 - 52: 34.122 distance: 43 - 74: 54.728 distance: 44 - 45: 23.805 distance: 45 - 46: 22.829 distance: 45 - 47: 30.719 distance: 46 - 48: 39.798 distance: 47 - 49: 11.405 distance: 48 - 50: 29.996 distance: 49 - 50: 57.263 distance: 50 - 51: 12.499 distance: 52 - 53: 22.218 distance: 53 - 54: 25.659 distance: 54 - 55: 33.396 distance: 54 - 60: 23.941 distance: 57 - 58: 39.169 distance: 57 - 59: 51.916 distance: 60 - 61: 26.837 distance: 61 - 62: 16.922 distance: 61 - 64: 41.183 distance: 62 - 63: 40.475 distance: 62 - 68: 17.922 distance: 64 - 65: 41.052 distance: 64 - 66: 56.584 distance: 65 - 67: 39.609 distance: 68 - 69: 40.015 distance: 69 - 70: 17.651 distance: 70 - 71: 29.240 distance: 70 - 74: 45.527 distance: 74 - 75: 27.081 distance: 75 - 76: 22.740 distance: 76 - 77: 40.051 distance: 76 - 78: 50.888 distance: 78 - 79: 15.537 distance: 79 - 80: 22.753 distance: 79 - 82: 53.207 distance: 80 - 81: 3.240 distance: 80 - 84: 28.679 distance: 81 - 107: 31.671 distance: 82 - 83: 8.784 distance: 84 - 85: 22.034 distance: 85 - 86: 23.809 distance: 85 - 88: 33.443 distance: 86 - 87: 7.357 distance: 86 - 90: 12.363 distance: 87 - 117: 22.907 distance: 88 - 89: 6.717 distance: 90 - 91: 22.615 distance: 91 - 92: 19.073 distance: 91 - 94: 22.216 distance: 92 - 93: 24.974 distance: 92 - 102: 40.072 distance: 93 - 123: 27.480 distance: 94 - 95: 5.137 distance: 95 - 96: 14.445 distance: 95 - 97: 3.043 distance: 96 - 98: 17.894 distance: 97 - 99: 11.396 distance: 98 - 100: 3.761 distance: 99 - 100: 18.037 distance: 100 - 101: 7.730 distance: 102 - 103: 44.762 distance: 103 - 104: 12.070 distance: 103 - 106: 45.027 distance: 104 - 107: 33.929 distance: 105 - 129: 33.456 distance: 110 - 135: 3.021