Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 21:15:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/04_2023/8hao_34598_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/04_2023/8hao_34598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/04_2023/8hao_34598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/04_2023/8hao_34598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/04_2023/8hao_34598_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/04_2023/8hao_34598_neut.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11745 2.51 5 N 3242 2.21 5 O 3372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 177": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I GLU 444": "OE1" <-> "OE2" Residue "I GLU 465": "OE1" <-> "OE2" Residue "I GLU 469": "OE1" <-> "OE2" Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 391": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "D" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "I" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2977 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 4 Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2960 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 11, 'TRANS': 348} Chain breaks: 4 Time building chain proxies: 9.67, per 1000 atoms: 0.52 Number of scatterers: 18479 At special positions: 0 Unit cell: (168.92, 143.376, 206, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3372 8.00 N 3242 7.00 C 11745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 107 " distance=2.05 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 117 " distance=2.03 Simple disulfide: pdb=" SG CYS I 108 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 170 " distance=2.03 Simple disulfide: pdb=" SG CYS I 281 " - pdb=" SG CYS I 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.04 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 2.8 seconds 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 42.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.509A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.762A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.449A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 298 through 320 removed outlier: 4.407A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 33 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.504A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.756A pdb=" N LEU C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 removed outlier: 4.399A pdb=" N TYR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 298 through 320 removed outlier: 4.061A pdb=" N SER C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.548A pdb=" N GLU D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.569A pdb=" N ASP E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.802A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.512A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 2 through 33 Processing helix chain 'I' and resid 33 through 51 Processing helix chain 'I' and resid 178 through 212 Processing helix chain 'I' and resid 217 through 246 Processing helix chain 'I' and resid 278 through 312 Processing helix chain 'I' and resid 316 through 347 removed outlier: 4.146A pdb=" N TRP I 322 " --> pdb=" O LYS I 318 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU I 331 " --> pdb=" O PHE I 327 " (cutoff:3.500A) Proline residue: I 332 - end of helix Processing helix chain 'I' and resid 357 through 359 No H-bonds generated for 'chain 'I' and resid 357 through 359' Processing helix chain 'I' and resid 360 through 392 Proline residue: I 366 - end of helix Processing helix chain 'I' and resid 400 through 418 Proline residue: I 415 - end of helix Processing helix chain 'I' and resid 419 through 425 removed outlier: 3.589A pdb=" N PHE I 424 " --> pdb=" O TYR I 421 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET I 425 " --> pdb=" O ILE I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 460 removed outlier: 3.913A pdb=" N SER I 449 " --> pdb=" O MET I 445 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY I 452 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE I 453 " --> pdb=" O SER I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 481 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.656A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 33 Processing helix chain 'R' and resid 33 through 51 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.531A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 246 Processing helix chain 'R' and resid 278 through 312 Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.231A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 392 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.053A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.852A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.789A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.833A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.870A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.666A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.696A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.660A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.514A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.817A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE C 222 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU C 39 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASP C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 45 through 52 removed outlier: 5.692A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER D 331 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.942A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.470A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.695A pdb=" N CYS D 166 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR D 179 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 168 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN D 175 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.708A pdb=" N SER D 189 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.523A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.537A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.245A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.235A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 148 through 149 987 hydrogen bonds defined for protein. 2847 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: 5.83 Time building geometry restraints manager: 7.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6030 1.35 - 1.47: 4785 1.47 - 1.59: 7905 1.59 - 1.72: 1 1.72 - 1.84: 172 Bond restraints: 18893 Sorted by residual: bond pdb=" CB PRO F 41 " pdb=" CG PRO F 41 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N PHE I 173 " pdb=" CA PHE I 173 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.41e-02 5.03e+03 5.52e+00 bond pdb=" N GLU D 3 " pdb=" CA GLU D 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N LEU C 5 " pdb=" CA LEU C 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 ... (remaining 18888 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.65: 245 105.65 - 112.82: 10031 112.82 - 119.99: 6528 119.99 - 127.16: 8538 127.16 - 134.33: 231 Bond angle restraints: 25573 Sorted by residual: angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 101.21 10.79 1.40e+00 5.10e-01 5.94e+01 angle pdb=" N PHE I 173 " pdb=" CA PHE I 173 " pdb=" C PHE I 173 " ideal model delta sigma weight residual 108.86 114.77 -5.91 1.41e+00 5.03e-01 1.76e+01 angle pdb=" C LYS I 172 " pdb=" N PHE I 173 " pdb=" CA PHE I 173 " ideal model delta sigma weight residual 122.53 116.44 6.09 1.61e+00 3.86e-01 1.43e+01 angle pdb=" N CYS R 108 " pdb=" CA CYS R 108 " pdb=" CB CYS R 108 " ideal model delta sigma weight residual 114.17 109.98 4.19 1.14e+00 7.69e-01 1.35e+01 angle pdb=" CA CYS R 48 " pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " ideal model delta sigma weight residual 114.40 121.81 -7.41 2.30e+00 1.89e-01 1.04e+01 ... (remaining 25568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 9723 17.61 - 35.21: 1133 35.21 - 52.82: 259 52.82 - 70.42: 47 70.42 - 88.03: 29 Dihedral angle restraints: 11191 sinusoidal: 4457 harmonic: 6734 Sorted by residual: dihedral pdb=" CB CYS F 99 " pdb=" SG CYS F 99 " pdb=" SG CYS F 107 " pdb=" CB CYS F 107 " ideal model delta sinusoidal sigma weight residual -86.00 0.43 -86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS I 131 " pdb=" SG CYS I 131 " pdb=" SG CYS I 170 " pdb=" CB CYS I 170 " ideal model delta sinusoidal sigma weight residual 93.00 170.66 -77.66 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS R 131 " pdb=" SG CYS R 131 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 170.32 -77.32 1 1.00e+01 1.00e-02 7.49e+01 ... (remaining 11188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1795 0.027 - 0.053: 652 0.053 - 0.080: 209 0.080 - 0.106: 82 0.106 - 0.133: 79 Chirality restraints: 2817 Sorted by residual: chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE D 93 " pdb=" N ILE D 93 " pdb=" C ILE D 93 " pdb=" CB ILE D 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL I 31 " pdb=" N VAL I 31 " pdb=" C VAL I 31 " pdb=" CB VAL I 31 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2814 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 172 " -0.027 2.00e-02 2.50e+03 5.37e-02 2.88e+01 pdb=" C LYS I 172 " 0.093 2.00e-02 2.50e+03 pdb=" O LYS I 172 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE I 173 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 40 " -0.073 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO F 41 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO F 41 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 41 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 106 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO D 107 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " 0.028 5.00e-02 4.00e+02 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 58 2.41 - 3.03: 11629 3.03 - 3.65: 27455 3.65 - 4.28: 40609 4.28 - 4.90: 70071 Nonbonded interactions: 149822 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 58 " model vdw 1.785 2.440 nonbonded pdb=" OE2 GLU A 266 " pdb=" OG1 THR C 48 " model vdw 1.899 2.440 nonbonded pdb=" O ALA I 242 " pdb=" OG SER I 246 " model vdw 1.974 2.440 nonbonded pdb=" OD2 ASP D 163 " pdb=" OG1 THR D 165 " model vdw 2.081 2.440 nonbonded pdb=" NE2 GLN D 75 " pdb=" O VAL D 100 " model vdw 2.188 2.520 ... (remaining 149817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = (chain 'I' and (resid 31 through 173 or resid 178 through 481)) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.180 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: 27.830 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.640 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 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 : 0.003 0.132 18893 Z= 0.167 Angle : 0.503 10.793 25573 Z= 0.282 Chirality : 0.037 0.133 2817 Planarity : 0.004 0.103 3251 Dihedral : 15.904 88.026 6803 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.92 % Rotamer Outliers : 0.40 % 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: 1.91 (0.18), residues: 2270 helix: 3.33 (0.17), residues: 915 sheet: 0.82 (0.25), residues: 452 loop : -0.76 (0.21), residues: 903 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 646 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 651 average time/residue: 0.3620 time to fit residues: 334.4072 Evaluate side-chains 479 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 28 GLN C 43 ASN D 62 HIS D 119 ASN D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 HIS H 10 ASN H 14 HIS H 16 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 HIS N 82 GLN N 84 ASN ** R 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS R 448 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 18893 Z= 0.274 Angle : 0.707 9.865 25573 Z= 0.371 Chirality : 0.045 0.262 2817 Planarity : 0.005 0.090 3251 Dihedral : 4.272 22.524 2536 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.44 % Favored : 96.39 % Rotamer Outliers : 5.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2270 helix: 2.56 (0.16), residues: 919 sheet: 0.64 (0.25), residues: 426 loop : -0.74 (0.21), residues: 925 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 592 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 51 residues processed: 650 average time/residue: 0.3451 time to fit residues: 327.0002 Evaluate side-chains 571 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 520 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.1847 time to fit residues: 20.0159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 43 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS I 139 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN P 9 HIS P 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 18893 Z= 0.266 Angle : 0.679 9.074 25573 Z= 0.364 Chirality : 0.045 0.273 2817 Planarity : 0.005 0.099 3251 Dihedral : 4.538 25.580 2536 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.17 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 2270 helix: 2.34 (0.16), residues: 917 sheet: 0.37 (0.24), residues: 436 loop : -0.78 (0.21), residues: 917 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 584 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 38 residues processed: 632 average time/residue: 0.3657 time to fit residues: 336.2641 Evaluate side-chains 581 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 543 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2258 time to fit residues: 18.0222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 218 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 195 optimal weight: 0.0010 chunk 58 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 234 GLN A 238 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN I 139 ASN I 295 ASN I 467 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18893 Z= 0.230 Angle : 0.674 10.796 25573 Z= 0.354 Chirality : 0.045 0.290 2817 Planarity : 0.004 0.070 3251 Dihedral : 4.453 26.634 2536 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer Outliers : 3.47 % 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: 1.04 (0.18), residues: 2270 helix: 2.34 (0.16), residues: 918 sheet: 0.32 (0.24), residues: 432 loop : -0.85 (0.21), residues: 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 573 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 43 residues processed: 607 average time/residue: 0.3565 time to fit residues: 309.2150 Evaluate side-chains 587 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 544 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2232 time to fit residues: 21.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 186 optimal weight: 0.0170 chunk 151 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 196 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 307 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 18893 Z= 0.195 Angle : 0.673 13.871 25573 Z= 0.350 Chirality : 0.044 0.270 2817 Planarity : 0.004 0.053 3251 Dihedral : 4.390 23.599 2536 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2270 helix: 2.35 (0.17), residues: 902 sheet: 0.39 (0.24), residues: 428 loop : -0.84 (0.21), residues: 940 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 555 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 31 residues processed: 574 average time/residue: 0.3664 time to fit residues: 301.8012 Evaluate side-chains 566 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 535 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2225 time to fit residues: 15.2916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 181 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 307 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 18893 Z= 0.229 Angle : 0.703 13.529 25573 Z= 0.367 Chirality : 0.046 0.338 2817 Planarity : 0.004 0.046 3251 Dihedral : 4.510 21.559 2536 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.90 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2270 helix: 2.20 (0.17), residues: 896 sheet: 0.20 (0.25), residues: 422 loop : -0.81 (0.21), residues: 952 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 567 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 591 average time/residue: 0.3843 time to fit residues: 322.8744 Evaluate side-chains 564 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 534 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2061 time to fit residues: 14.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 GLN G 44 HIS ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.7937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 18893 Z= 0.243 Angle : 0.722 14.732 25573 Z= 0.375 Chirality : 0.045 0.241 2817 Planarity : 0.004 0.046 3251 Dihedral : 4.571 21.880 2536 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2270 helix: 2.06 (0.17), residues: 903 sheet: 0.11 (0.25), residues: 432 loop : -0.85 (0.21), residues: 935 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 565 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 26 residues processed: 587 average time/residue: 0.3753 time to fit residues: 317.4801 Evaluate side-chains 566 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 540 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1790 time to fit residues: 11.2731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 148 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 171 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.8391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 18893 Z= 0.253 Angle : 0.772 15.567 25573 Z= 0.403 Chirality : 0.047 0.269 2817 Planarity : 0.004 0.043 3251 Dihedral : 4.747 25.991 2536 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.24 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2270 helix: 1.79 (0.17), residues: 916 sheet: 0.15 (0.26), residues: 408 loop : -0.91 (0.21), residues: 946 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 561 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 30 residues processed: 574 average time/residue: 0.3641 time to fit residues: 299.1062 Evaluate side-chains 575 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 545 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1797 time to fit residues: 12.5984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 214 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 62 HIS ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 18893 Z= 0.237 Angle : 0.769 14.550 25573 Z= 0.401 Chirality : 0.047 0.235 2817 Planarity : 0.004 0.056 3251 Dihedral : 4.727 23.272 2536 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.14 % Favored : 95.73 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2270 helix: 1.69 (0.17), residues: 916 sheet: -0.02 (0.25), residues: 430 loop : -0.92 (0.21), residues: 924 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 552 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 561 average time/residue: 0.3616 time to fit residues: 289.8602 Evaluate side-chains 538 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 528 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2062 time to fit residues: 6.2164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.2980 chunk 101 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.8948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 18893 Z= 0.253 Angle : 0.818 15.587 25573 Z= 0.421 Chirality : 0.047 0.264 2817 Planarity : 0.005 0.051 3251 Dihedral : 4.769 23.591 2536 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.11 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2270 helix: 1.64 (0.17), residues: 905 sheet: 0.04 (0.25), residues: 426 loop : -1.06 (0.21), residues: 939 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 552 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 556 average time/residue: 0.3843 time to fit residues: 306.2759 Evaluate side-chains 552 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 537 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2109 time to fit residues: 8.3927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.149202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.124512 restraints weight = 36048.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.128477 restraints weight = 19292.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.131055 restraints weight = 12118.532| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.9124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 18893 Z= 0.241 Angle : 0.815 15.742 25573 Z= 0.418 Chirality : 0.047 0.253 2817 Planarity : 0.005 0.064 3251 Dihedral : 4.742 25.564 2536 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.51 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2270 helix: 1.52 (0.17), residues: 917 sheet: -0.03 (0.25), residues: 430 loop : -1.08 (0.21), residues: 923 =============================================================================== Job complete usr+sys time: 5688.12 seconds wall clock time: 103 minutes 16.52 seconds (6196.52 seconds total)