Starting phenix.real_space_refine (version: dev) on Wed Feb 22 05:44:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhq_32003/02_2023/7vhq_32003.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhq_32003/02_2023/7vhq_32003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhq_32003/02_2023/7vhq_32003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhq_32003/02_2023/7vhq_32003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhq_32003/02_2023/7vhq_32003.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhq_32003/02_2023/7vhq_32003.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "E TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 181": "OD1" <-> "OD2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G ASP 125": "OD1" <-> "OD2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 221": "OE1" <-> "OE2" Residue "G GLU 274": "OE1" <-> "OE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 48": "OE1" <-> "OE2" Residue "e ASP 62": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16650 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "F" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "G" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "H" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "U" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "e" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "f" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Time building chain proxies: 9.69, per 1000 atoms: 0.58 Number of scatterers: 16650 At special positions: 0 Unit cell: (176.519, 130.011, 171.234, 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 45 16.00 O 3186 8.00 N 2973 7.00 C 10446 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: 6.27 Conformation dependent library (CDL) restraints added in 2.4 seconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 29 sheets defined 54.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'C' and resid 33 through 43 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 Processing helix chain 'D' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 96 Processing helix chain 'E' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 199 removed outlier: 3.719A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Proline residue: E 277 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 96 Processing helix chain 'F' and resid 169 through 176 Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 200 through 208 Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'F' and resid 244 through 246 No H-bonds generated for 'chain 'F' and resid 244 through 246' Processing helix chain 'F' and resid 247 through 318 removed outlier: 4.059A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Proline residue: F 277 - end of helix Proline residue: F 313 - end of helix removed outlier: 3.750A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 removed outlier: 3.505A pdb=" N ILE G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 145 through 157 Processing helix chain 'G' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR G 294 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 326 removed outlier: 4.518A pdb=" N TYR G 325 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 111 through 134 removed outlier: 4.347A pdb=" N ALA H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 146 through 156 Processing helix chain 'H' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 307 removed outlier: 3.523A pdb=" N TYR H 294 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR H 325 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY I 132 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER I 143 " --> pdb=" O ILE I 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY I 145 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 158 Processing helix chain 'I' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL I 234 " --> pdb=" O GLU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 307 Processing helix chain 'I' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR I 325 " --> pdb=" O PHE I 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 96 Processing helix chain 'U' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR U 173 " --> pdb=" O ASN U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS U 198 " --> pdb=" O GLY U 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 199 " --> pdb=" O VAL U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG U 209 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR U 210 " --> pdb=" O THR U 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL U 211 " --> pdb=" O GLU U 207 " (cutoff:3.500A) Proline residue: U 226 - end of helix Processing helix chain 'U' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA U 249 " --> pdb=" O GLU U 245 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA U 250 " --> pdb=" O GLU U 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN U 262 " --> pdb=" O ARG U 258 " (cutoff:3.500A) Proline residue: U 277 - end of helix Proline residue: U 313 - end of helix removed outlier: 3.558A pdb=" N ALA U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR U 322 " --> pdb=" O ALA U 318 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 338 " --> pdb=" O VAL U 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 43 removed outlier: 3.593A pdb=" N PHE e 37 " --> pdb=" O ASP e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU e 78 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP e 79 " --> pdb=" O PRO e 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 43 Processing helix chain 'f' and resid 75 through 84 removed outlier: 4.186A pdb=" N ASP f 79 " --> pdb=" O PRO f 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR A 69 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG A 47 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 89 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 49 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B 47 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 89 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 49 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG C 47 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 89 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 49 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG D 47 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 89 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 49 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'E' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG E 110 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 131 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU E 160 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG E 166 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU E 233 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 339 through 341 removed outlier: 5.801A pdb=" N ARG F 339 " --> pdb=" O MET G 314 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS E 340 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL G 315 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 339 " --> pdb=" O MET H 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET H 316 " --> pdb=" O ARG E 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 341 " --> pdb=" O MET H 316 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET I 314 " --> pdb=" O VAL U 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'F' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG F 110 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS F 116 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG F 158 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA F 240 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 160 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE F 238 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN F 162 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 236 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN F 164 " --> pdb=" O LEU F 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AB4, first strand: chain 'G' and resid 27 through 33 Processing sheet with id=AB5, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'G' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER G 91 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA G 76 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 89 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG G 78 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 87 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 88 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE G 213 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP G 90 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 207 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG G 96 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL G 205 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.638A pdb=" N LYS H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA H 76 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL H 89 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG H 78 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 87 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE H 88 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 212 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP H 90 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE H 210 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR H 92 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 208 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS H 94 " --> pdb=" O VAL H 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'I' and resid 27 through 28 Processing sheet with id=AC4, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR I 92 " --> pdb=" O ILE I 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE I 210 " --> pdb=" O TYR I 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS I 94 " --> pdb=" O VAL I 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL I 208 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG I 96 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 206 " --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 97 through 100 Processing sheet with id=AC8, first strand: chain 'U' and resid 116 through 118 Processing sheet with id=AC9, first strand: chain 'U' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU U 160 " --> pdb=" O GLN U 239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG U 166 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU U 233 " --> pdb=" O ARG U 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG e 47 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL e 89 " --> pdb=" O ARG e 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA e 49 " --> pdb=" O VAL e 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG f 47 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL f 89 " --> pdb=" O ARG f 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA f 49 " --> pdb=" O VAL f 89 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 3033 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: 5.00 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4497 1.33 - 1.45: 2612 1.45 - 1.57: 9691 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 16890 Sorted by residual: bond pdb=" CA ILE C 70 " pdb=" CB ILE C 70 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.55e-02 4.16e+03 1.19e+00 bond pdb=" CG GLN A 39 " pdb=" CD GLN A 39 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CA GLN E 276 " pdb=" C GLN E 276 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.06e+00 bond pdb=" C LYS F 133 " pdb=" O LYS F 133 " ideal model delta sigma weight residual 1.248 1.236 0.013 1.26e-02 6.30e+03 1.02e+00 bond pdb=" CA GLN F 276 " pdb=" C GLN F 276 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.23e-02 6.61e+03 9.74e-01 ... (remaining 16885 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.05: 262 105.05 - 112.27: 8497 112.27 - 119.49: 5578 119.49 - 126.71: 8358 126.71 - 133.93: 108 Bond angle restraints: 22803 Sorted by residual: angle pdb=" C ASN e 43 " pdb=" N ASP e 44 " pdb=" CA ASP e 44 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N GLN A 39 " pdb=" CA GLN A 39 " pdb=" CB GLN A 39 " ideal model delta sigma weight residual 110.39 116.02 -5.63 1.66e+00 3.63e-01 1.15e+01 angle pdb=" N ILE C 70 " pdb=" CA ILE C 70 " pdb=" CB ILE C 70 " ideal model delta sigma weight residual 110.23 113.75 -3.52 1.07e+00 8.73e-01 1.08e+01 angle pdb=" C LEU A 38 " pdb=" N GLN A 39 " pdb=" CA GLN A 39 " ideal model delta sigma weight residual 120.72 115.25 5.47 1.67e+00 3.59e-01 1.07e+01 angle pdb=" CA GLN A 39 " pdb=" CB GLN A 39 " pdb=" CG GLN A 39 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 ... (remaining 22798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 9385 17.00 - 34.00: 918 34.00 - 50.99: 151 50.99 - 67.99: 15 67.99 - 84.99: 16 Dihedral angle restraints: 10485 sinusoidal: 4383 harmonic: 6102 Sorted by residual: dihedral pdb=" CA GLY U 208 " pdb=" C GLY U 208 " pdb=" N ARG U 209 " pdb=" CA ARG U 209 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY I 35 " pdb=" C GLY I 35 " pdb=" N LYS I 36 " pdb=" CA LYS I 36 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASN U 169 " pdb=" C ASN U 169 " pdb=" N PRO U 170 " pdb=" CA PRO U 170 " ideal model delta harmonic sigma weight residual 180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 10482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1856 0.037 - 0.075: 465 0.075 - 0.112: 212 0.112 - 0.150: 50 0.150 - 0.187: 6 Chirality restraints: 2589 Sorted by residual: chirality pdb=" CA ASP e 44 " pdb=" N ASP e 44 " pdb=" C ASP e 44 " pdb=" CB ASP e 44 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLN e 39 " pdb=" N GLN e 39 " pdb=" C GLN e 39 " pdb=" CB GLN e 39 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 2586 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 194 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 195 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 74 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 75 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN e 43 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C ASN e 43 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN e 43 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP e 44 " 0.009 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 487 2.71 - 3.26: 17159 3.26 - 3.81: 26696 3.81 - 4.35: 31457 4.35 - 4.90: 54908 Nonbonded interactions: 130707 Sorted by model distance: nonbonded pdb=" OE1 GLU e 40 " pdb=" OH TYR e 66 " model vdw 2.165 2.440 nonbonded pdb=" O LYS F 172 " pdb=" OG SER F 176 " model vdw 2.180 2.440 nonbonded pdb=" OG SER I 143 " pdb=" NH2 ARG U 193 " model vdw 2.210 2.520 nonbonded pdb=" OE1 GLN E 164 " pdb=" NZ LYS G 122 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASP G 285 " pdb=" N ALA G 286 " model vdw 2.247 2.520 ... (remaining 130702 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10446 2.51 5 N 2973 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.900 Check model and map are aligned: 0.230 Process input model: 43.210 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 0.027 16890 Z= 0.192 Angle : 0.603 7.570 22803 Z= 0.342 Chirality : 0.043 0.187 2589 Planarity : 0.004 0.076 2985 Dihedral : 13.433 84.989 6525 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2046 helix: 2.44 (0.16), residues: 1037 sheet: 0.93 (0.30), residues: 342 loop : -0.67 (0.23), residues: 667 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2849 time to fit residues: 121.9787 Evaluate side-chains 245 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 80 ASN F 116 HIS I 70 GLN e 39 GLN e 43 ASN e 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 16890 Z= 0.185 Angle : 0.535 8.417 22803 Z= 0.288 Chirality : 0.043 0.185 2589 Planarity : 0.004 0.053 2985 Dihedral : 4.089 21.188 2331 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.16 % 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: 1.97 (0.19), residues: 2046 helix: 2.57 (0.15), residues: 1050 sheet: 0.81 (0.27), residues: 381 loop : -0.65 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 266 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 270 average time/residue: 0.2882 time to fit residues: 116.9365 Evaluate side-chains 250 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 237 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1558 time to fit residues: 6.5951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 64 ASN B 80 ASN D 42 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 16890 Z= 0.216 Angle : 0.529 9.685 22803 Z= 0.286 Chirality : 0.043 0.175 2589 Planarity : 0.003 0.042 2985 Dihedral : 4.063 21.587 2331 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.33 % 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: 1.95 (0.19), residues: 2046 helix: 2.56 (0.15), residues: 1051 sheet: 0.81 (0.27), residues: 380 loop : -0.68 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 258 average time/residue: 0.2937 time to fit residues: 113.4015 Evaluate side-chains 245 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1991 time to fit residues: 6.4718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 122 optimal weight: 0.0570 chunk 183 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** U 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16890 Z= 0.179 Angle : 0.524 7.834 22803 Z= 0.281 Chirality : 0.043 0.175 2589 Planarity : 0.003 0.037 2985 Dihedral : 4.010 21.221 2331 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.66 % 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: 2.03 (0.19), residues: 2046 helix: 2.63 (0.15), residues: 1050 sheet: 0.89 (0.27), residues: 374 loop : -0.68 (0.24), residues: 622 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 254 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 265 average time/residue: 0.2891 time to fit residues: 116.1774 Evaluate side-chains 249 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1591 time to fit residues: 7.2566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.0270 chunk 165 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 80 ASN C 52 ASN C 80 ASN D 42 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 16890 Z= 0.270 Angle : 0.563 11.817 22803 Z= 0.302 Chirality : 0.044 0.193 2589 Planarity : 0.003 0.036 2985 Dihedral : 4.129 20.973 2331 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 1.16 % 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: 1.88 (0.19), residues: 2046 helix: 2.57 (0.15), residues: 1045 sheet: 0.76 (0.27), residues: 380 loop : -0.79 (0.24), residues: 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 253 average time/residue: 0.2835 time to fit residues: 108.8841 Evaluate side-chains 244 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1513 time to fit residues: 6.5426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16890 Z= 0.201 Angle : 0.550 9.873 22803 Z= 0.294 Chirality : 0.043 0.216 2589 Planarity : 0.003 0.033 2985 Dihedral : 4.056 21.055 2331 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2046 helix: 2.65 (0.15), residues: 1040 sheet: 0.88 (0.27), residues: 374 loop : -0.70 (0.24), residues: 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 251 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 260 average time/residue: 0.2855 time to fit residues: 112.5451 Evaluate side-chains 243 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1470 time to fit residues: 4.7198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 80 ASN C 64 ASN C 80 ASN D 42 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16890 Z= 0.262 Angle : 0.574 11.336 22803 Z= 0.309 Chirality : 0.044 0.267 2589 Planarity : 0.003 0.032 2985 Dihedral : 4.149 20.837 2331 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 2046 helix: 2.57 (0.15), residues: 1046 sheet: 0.83 (0.27), residues: 374 loop : -0.83 (0.24), residues: 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 248 average time/residue: 0.2947 time to fit residues: 109.8751 Evaluate side-chains 243 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1565 time to fit residues: 5.7913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 123 optimal weight: 0.0370 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 152 optimal weight: 0.3980 chunk 176 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN ** U 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16890 Z= 0.189 Angle : 0.564 13.419 22803 Z= 0.300 Chirality : 0.043 0.313 2589 Planarity : 0.003 0.031 2985 Dihedral : 4.046 21.321 2331 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2046 helix: 2.67 (0.15), residues: 1046 sheet: 0.91 (0.27), residues: 374 loop : -0.77 (0.24), residues: 626 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 249 average time/residue: 0.2887 time to fit residues: 109.1146 Evaluate side-chains 237 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1682 time to fit residues: 3.3848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 80 ASN C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 16890 Z= 0.333 Angle : 0.621 13.255 22803 Z= 0.331 Chirality : 0.045 0.321 2589 Planarity : 0.004 0.032 2985 Dihedral : 4.299 22.532 2331 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.72 % 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: 1.79 (0.19), residues: 2046 helix: 2.49 (0.15), residues: 1047 sheet: 0.81 (0.27), residues: 374 loop : -0.90 (0.24), residues: 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 241 average time/residue: 0.2880 time to fit residues: 103.9666 Evaluate side-chains 236 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1524 time to fit residues: 4.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 0.0030 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 16890 Z= 0.223 Angle : 0.592 11.731 22803 Z= 0.314 Chirality : 0.044 0.234 2589 Planarity : 0.003 0.032 2985 Dihedral : 4.199 25.433 2331 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.22 % 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: 1.89 (0.19), residues: 2046 helix: 2.60 (0.15), residues: 1047 sheet: 0.82 (0.27), residues: 374 loop : -0.87 (0.24), residues: 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 237 average time/residue: 0.2924 time to fit residues: 104.7510 Evaluate side-chains 227 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1407 time to fit residues: 3.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 163 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 80 ASN B 85 ASN C 80 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069200 restraints weight = 44023.650| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.74 r_work: 0.3092 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 16890 Z= 0.283 Angle : 0.603 11.395 22803 Z= 0.323 Chirality : 0.044 0.223 2589 Planarity : 0.003 0.031 2985 Dihedral : 4.230 20.891 2331 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.50 % 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: 1.79 (0.19), residues: 2046 helix: 2.53 (0.15), residues: 1046 sheet: 0.75 (0.27), residues: 374 loop : -0.92 (0.24), residues: 626 =============================================================================== Job complete usr+sys time: 3550.13 seconds wall clock time: 64 minutes 42.47 seconds (3882.47 seconds total)