Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 00:33:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li3_0902/10_2023/6li3_0902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li3_0902/10_2023/6li3_0902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li3_0902/10_2023/6li3_0902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li3_0902/10_2023/6li3_0902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li3_0902/10_2023/6li3_0902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li3_0902/10_2023/6li3_0902.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 57 5.16 5 C 5267 2.51 5 N 1436 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 157": "NH1" <-> "NH2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 188": "OD1" <-> "OD2" Residue "R TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "R TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 333": "OE1" <-> "OE2" Residue "A ASP 11": "OD1" <-> "OD2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8289 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1989 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} 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: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 4.69, per 1000 atoms: 0.57 Number of scatterers: 8289 At special positions: 0 Unit cell: (98.1, 131.89, 82.84, 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 57 16.00 O 1529 8.00 N 1436 7.00 C 5267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 193 " 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 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: 3.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 40.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 74 through 104 removed outlier: 3.781A pdb=" N LEU R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL R 96 " --> pdb=" O VAL R 92 " (cutoff:3.500A) Proline residue: R 97 - end of helix removed outlier: 4.107A pdb=" N LEU R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 145 removed outlier: 4.269A pdb=" N LEU R 112 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU R 124 " --> pdb=" O ILE R 120 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER R 126 " --> pdb=" O SER R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 172 removed outlier: 3.847A pdb=" N CYS R 170 " --> pdb=" O TRP R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 178 Processing helix chain 'R' and resid 191 through 196 Processing helix chain 'R' and resid 200 through 210 removed outlier: 3.875A pdb=" N VAL R 208 " --> pdb=" O THR R 204 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU R 210 " --> pdb=" O PHE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 244 removed outlier: 4.557A pdb=" N VAL R 219 " --> pdb=" O ALA R 215 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 226 " --> pdb=" O THR R 222 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU R 236 " --> pdb=" O GLN R 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 290 removed outlier: 4.034A pdb=" N PHE R 274 " --> pdb=" O ILE R 270 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) Proline residue: R 280 - end of helix removed outlier: 3.775A pdb=" N SER R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 307 removed outlier: 3.834A pdb=" N LEU R 301 " --> pdb=" O THR R 297 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE R 307 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 321 Proline residue: R 314 - end of helix removed outlier: 4.130A pdb=" N ASN R 321 " --> pdb=" O TYR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 337 removed outlier: 3.652A pdb=" N ARG R 329 " --> pdb=" O ARG R 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR R 334 " --> pdb=" O ARG R 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.731A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.762A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.246A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.928A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.608A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 346 removed outlier: 3.640A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.669A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 353' Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.689A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.607A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.157A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 211 removed outlier: 4.152A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.058A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.088A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.289A 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: 3.524A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.917A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.528A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.522A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.985A 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: 6.625A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.745A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.546A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 3.38 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: 2697 1.35 - 1.46: 2042 1.46 - 1.58: 3657 1.58 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8472 Sorted by residual: bond pdb=" C VAL N 12 " pdb=" N GLN N 13 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.47e-02 4.63e+03 2.60e+00 bond pdb=" CA ILE R 189 " pdb=" CB ILE R 189 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.87e-01 bond pdb=" CA ASN R 313 " pdb=" C ASN R 313 " ideal model delta sigma weight residual 1.521 1.532 -0.011 1.14e-02 7.69e+03 8.91e-01 bond pdb=" C ILE R 121 " pdb=" O ILE R 121 " ideal model delta sigma weight residual 1.233 1.243 -0.010 1.22e-02 6.72e+03 6.15e-01 bond pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 1.469 1.474 -0.006 7.40e-03 1.83e+04 6.02e-01 ... (remaining 8467 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.29: 236 107.29 - 113.96: 4736 113.96 - 120.63: 3392 120.63 - 127.30: 3033 127.30 - 133.97: 88 Bond angle restraints: 11485 Sorted by residual: angle pdb=" C ILE R 54 " pdb=" CA ILE R 54 " pdb=" CB ILE R 54 " ideal model delta sigma weight residual 111.97 108.04 3.93 1.28e+00 6.10e-01 9.41e+00 angle pdb=" N GLY N 9 " pdb=" CA GLY N 9 " pdb=" C GLY N 9 " ideal model delta sigma weight residual 111.21 113.77 -2.56 1.04e+00 9.25e-01 6.08e+00 angle pdb=" N ILE R 189 " pdb=" CA ILE R 189 " pdb=" C ILE R 189 " ideal model delta sigma weight residual 106.55 109.73 -3.18 1.45e+00 4.76e-01 4.80e+00 angle pdb=" C LEU R 71 " pdb=" N HIS R 72 " pdb=" CA HIS R 72 " ideal model delta sigma weight residual 120.79 123.77 -2.98 1.39e+00 5.18e-01 4.58e+00 angle pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" C VAL A 224 " ideal model delta sigma weight residual 107.51 110.70 -3.19 1.49e+00 4.50e-01 4.58e+00 ... (remaining 11480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4513 17.71 - 35.42: 421 35.42 - 53.13: 70 53.13 - 70.83: 10 70.83 - 88.54: 7 Dihedral angle restraints: 5021 sinusoidal: 1975 harmonic: 3046 Sorted by residual: dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual -86.00 -124.55 38.55 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 785 0.030 - 0.059: 367 0.059 - 0.089: 89 0.089 - 0.119: 46 0.119 - 0.149: 4 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1288 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 174 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO R 175 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 313 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO R 314 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 314 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 314 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 332 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.016 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 150 2.68 - 3.23: 7621 3.23 - 3.79: 12547 3.79 - 4.34: 16315 4.34 - 4.90: 26829 Nonbonded interactions: 63462 Sorted by model distance: nonbonded pdb=" OD1 ASP R 138 " pdb=" OH TYR R 149 " model vdw 2.124 2.440 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR A 40 " model vdw 2.165 2.440 nonbonded pdb=" O GLU R 191 " pdb=" OG1 THR R 195 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.244 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.256 2.440 ... (remaining 63457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.840 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: 4.080 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 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 : 0.002 0.039 8472 Z= 0.134 Angle : 0.558 5.657 11485 Z= 0.344 Chirality : 0.038 0.149 1291 Planarity : 0.003 0.037 1459 Dihedral : 13.864 88.543 3044 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -2.69 (0.22), residues: 1031 helix: -1.04 (0.23), residues: 413 sheet: -0.90 (0.33), residues: 200 loop : -2.97 (0.23), residues: 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.061 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2436 time to fit residues: 86.5655 Evaluate side-chains 193 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 GLN R 309 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 278 ASN A 371 ASN A 387 HIS B 6 GLN B 16 ASN B 44 GLN B 62 HIS B 91 HIS B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN G 18 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8472 Z= 0.201 Angle : 0.571 9.900 11485 Z= 0.287 Chirality : 0.040 0.162 1291 Planarity : 0.004 0.041 1459 Dihedral : 3.359 22.061 1144 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.21 % Allowed : 16.54 % Favored : 81.26 % 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: -1.58 (0.24), residues: 1031 helix: 0.22 (0.26), residues: 419 sheet: -0.88 (0.33), residues: 196 loop : -2.46 (0.25), residues: 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 205 average time/residue: 0.2153 time to fit residues: 60.4467 Evaluate side-chains 189 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0746 time to fit residues: 3.2104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8472 Z= 0.163 Angle : 0.521 8.946 11485 Z= 0.262 Chirality : 0.040 0.150 1291 Planarity : 0.004 0.043 1459 Dihedral : 3.351 22.536 1144 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.21 % Allowed : 19.85 % Favored : 78.94 % 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: -0.93 (0.25), residues: 1031 helix: 0.79 (0.27), residues: 418 sheet: -0.05 (0.35), residues: 196 loop : -2.43 (0.26), residues: 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 0.955 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 183 average time/residue: 0.2072 time to fit residues: 51.6078 Evaluate side-chains 171 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0781 time to fit residues: 2.4988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 HIS ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 294 GLN B 88 ASN B 225 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8472 Z= 0.309 Angle : 0.619 10.837 11485 Z= 0.322 Chirality : 0.043 0.157 1291 Planarity : 0.004 0.049 1459 Dihedral : 3.985 21.750 1144 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.65 % Allowed : 22.49 % Favored : 74.86 % 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: -0.79 (0.26), residues: 1031 helix: 0.78 (0.26), residues: 419 sheet: -0.08 (0.37), residues: 195 loop : -2.14 (0.27), residues: 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 193 average time/residue: 0.2217 time to fit residues: 57.7594 Evaluate side-chains 169 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0795 time to fit residues: 3.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8472 Z= 0.219 Angle : 0.570 9.581 11485 Z= 0.291 Chirality : 0.042 0.253 1291 Planarity : 0.004 0.047 1459 Dihedral : 3.825 22.643 1144 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.32 % Allowed : 25.47 % Favored : 72.22 % 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: -0.51 (0.26), residues: 1031 helix: 1.05 (0.27), residues: 418 sheet: 0.06 (0.36), residues: 207 loop : -2.07 (0.28), residues: 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 178 average time/residue: 0.2122 time to fit residues: 51.2813 Evaluate side-chains 168 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0793 time to fit residues: 2.8671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8472 Z= 0.179 Angle : 0.545 7.548 11485 Z= 0.279 Chirality : 0.041 0.177 1291 Planarity : 0.004 0.049 1459 Dihedral : 3.698 22.134 1144 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.54 % Allowed : 25.25 % Favored : 72.22 % 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: -0.29 (0.26), residues: 1031 helix: 1.22 (0.27), residues: 415 sheet: 0.25 (0.37), residues: 193 loop : -1.90 (0.27), residues: 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 0.958 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 185 average time/residue: 0.2063 time to fit residues: 52.4200 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0861 time to fit residues: 3.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 GLN ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8472 Z= 0.169 Angle : 0.542 8.221 11485 Z= 0.278 Chirality : 0.042 0.276 1291 Planarity : 0.003 0.048 1459 Dihedral : 3.646 22.437 1144 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.32 % Allowed : 26.79 % Favored : 71.89 % 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: -0.21 (0.26), residues: 1031 helix: 1.26 (0.27), residues: 417 sheet: 0.30 (0.38), residues: 193 loop : -1.85 (0.28), residues: 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.008 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 179 average time/residue: 0.2109 time to fit residues: 51.6678 Evaluate side-chains 172 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0909 time to fit residues: 2.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 chunk 94 optimal weight: 0.0870 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8472 Z= 0.152 Angle : 0.554 13.475 11485 Z= 0.280 Chirality : 0.041 0.187 1291 Planarity : 0.003 0.049 1459 Dihedral : 3.541 21.708 1144 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.10 % Allowed : 27.01 % Favored : 71.89 % 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: -0.17 (0.26), residues: 1031 helix: 1.35 (0.27), residues: 417 sheet: 0.30 (0.37), residues: 192 loop : -1.88 (0.28), residues: 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 175 average time/residue: 0.2118 time to fit residues: 50.4701 Evaluate side-chains 172 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0919 time to fit residues: 2.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.0170 chunk 28 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8472 Z= 0.157 Angle : 0.544 8.811 11485 Z= 0.281 Chirality : 0.041 0.189 1291 Planarity : 0.003 0.049 1459 Dihedral : 3.452 21.894 1144 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.88 % Allowed : 27.34 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1031 helix: 1.40 (0.27), residues: 417 sheet: 0.28 (0.37), residues: 194 loop : -1.79 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 171 average time/residue: 0.2223 time to fit residues: 51.2530 Evaluate side-chains 170 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1003 time to fit residues: 2.3443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8472 Z= 0.292 Angle : 0.626 9.160 11485 Z= 0.325 Chirality : 0.044 0.186 1291 Planarity : 0.004 0.047 1459 Dihedral : 3.834 21.995 1144 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.55 % Allowed : 28.22 % Favored : 71.22 % 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: -0.33 (0.26), residues: 1031 helix: 1.19 (0.26), residues: 419 sheet: 0.04 (0.36), residues: 211 loop : -1.92 (0.28), residues: 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 164 average time/residue: 0.2258 time to fit residues: 49.8666 Evaluate side-chains 160 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0943 time to fit residues: 1.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.194450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143947 restraints weight = 9543.855| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.19 r_work: 0.3507 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8472 Z= 0.185 Angle : 0.575 8.626 11485 Z= 0.293 Chirality : 0.042 0.189 1291 Planarity : 0.004 0.048 1459 Dihedral : 3.680 21.909 1144 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.33 % Allowed : 28.45 % Favored : 71.22 % 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: -0.12 (0.26), residues: 1031 helix: 1.39 (0.26), residues: 417 sheet: 0.22 (0.37), residues: 196 loop : -1.80 (0.28), residues: 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2139.63 seconds wall clock time: 39 minutes 26.33 seconds (2366.33 seconds total)