Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 10:15:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/04_2023/7tyh_26179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/04_2023/7tyh_26179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/04_2023/7tyh_26179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/04_2023/7tyh_26179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/04_2023/7tyh_26179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyh_26179/04_2023/7tyh_26179_updated.pdb" } resolution = 3.3 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= 0.003 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 68 5.16 5 C 6015 2.51 5 N 1663 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "R GLU 240": "OE1" <-> "OE2" Residue "R GLU 397": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9492 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 514 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 186 Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29} Chain: "R" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2867 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 5.41, per 1000 atoms: 0.57 Number of scatterers: 9492 At special positions: 0 Unit cell: (89.88, 102.72, 156.648, 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 68 16.00 O 1746 8.00 N 1663 7.00 C 6015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.01 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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: 3.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 12 sheets defined 35.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.797A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.583A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.611A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.843A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.248A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.556A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 removed outlier: 3.518A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.821A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 33 No H-bonds generated for 'chain 'G' and resid 30 through 33' Processing helix chain 'G' and resid 35 through 43 removed outlier: 3.582A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.608A pdb=" N GLN E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 103 removed outlier: 4.193A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 126 removed outlier: 3.602A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 165 removed outlier: 3.531A pdb=" N ALA E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Proline residue: E 153 - end of helix removed outlier: 3.603A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.551A pdb=" N LEU E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 21 removed outlier: 3.659A pdb=" N ASN P 17 " --> pdb=" O THR P 13 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS P 20 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 61 removed outlier: 3.753A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 135 No H-bonds generated for 'chain 'R' and resid 132 through 135' Processing helix chain 'R' and resid 138 through 170 removed outlier: 3.572A pdb=" N LYS R 143 " --> pdb=" O PRO R 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 148 " --> pdb=" O ASN R 144 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE R 170 " --> pdb=" O SER R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 204 removed outlier: 3.720A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 213 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.620A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 244 " --> pdb=" O GLU R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 267 removed outlier: 3.584A pdb=" N TRP R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 283 Proline residue: R 273 - end of helix removed outlier: 3.749A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR R 280 " --> pdb=" O HIS R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 316 removed outlier: 3.687A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 4.126A pdb=" N LEU R 309 " --> pdb=" O MET R 306 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL R 310 " --> pdb=" O ALA R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 328 Processing helix chain 'R' and resid 334 through 337 No H-bonds generated for 'chain 'R' and resid 334 through 337' Processing helix chain 'R' and resid 339 through 343 removed outlier: 3.798A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 339 through 343' Processing helix chain 'R' and resid 345 through 352 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 366 through 388 removed outlier: 4.666A pdb=" N ILE R 371 " --> pdb=" O MET R 367 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS R 377 " --> pdb=" O ASP R 373 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU R 379 " --> pdb=" O VAL R 375 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE R 385 " --> pdb=" O HIS R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 399 No H-bonds generated for 'chain 'R' and resid 396 through 399' Processing helix chain 'R' and resid 401 through 404 No H-bonds generated for 'chain 'R' and resid 401 through 404' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.339A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.919A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.924A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.155A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.553A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.927A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 5 Processing sheet with id= K, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.515A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.515A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 894 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: 2.57 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1556 1.31 - 1.44: 2704 1.44 - 1.56: 5345 1.56 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9700 Sorted by residual: bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.237 1.189 0.049 1.26e-02 6.30e+03 1.49e+01 bond pdb=" N ARG N 98 " pdb=" CA ARG N 98 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.21e-02 6.83e+03 1.36e+01 bond pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.22e-02 6.72e+03 1.24e+01 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" N CYS P 7 " pdb=" CA CYS P 7 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.22e+00 ... (remaining 9695 not shown) Histogram of bond angle deviations from ideal: 100.21 - 107.12: 273 107.12 - 114.04: 5448 114.04 - 120.95: 4505 120.95 - 127.86: 2864 127.86 - 134.78: 89 Bond angle restraints: 13179 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 100.21 11.79 1.40e+00 5.10e-01 7.09e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 111.77 120.11 -8.34 1.67e+00 3.59e-01 2.49e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" O PRO N 102 " ideal model delta sigma weight residual 122.13 116.49 5.64 1.23e+00 6.61e-01 2.10e+01 angle pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" O VAL N 110 " ideal model delta sigma weight residual 120.85 116.37 4.48 1.06e+00 8.90e-01 1.78e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" N PHE N 103 " ideal model delta sigma weight residual 114.58 119.39 -4.81 1.16e+00 7.43e-01 1.72e+01 ... (remaining 13174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5337 17.98 - 35.97: 336 35.97 - 53.95: 58 53.95 - 71.93: 12 71.93 - 89.91: 6 Dihedral angle restraints: 5749 sinusoidal: 2117 harmonic: 3632 Sorted by residual: dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 154.15 -61.15 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -127.86 41.86 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " pdb=" OD1 ASP N 106 " ideal model delta sinusoidal sigma weight residual -30.00 -87.44 57.44 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1085 0.041 - 0.081: 274 0.081 - 0.122: 104 0.122 - 0.163: 14 0.163 - 0.204: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA MET P 8 " pdb=" N MET P 8 " pdb=" C MET P 8 " pdb=" CB MET P 8 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA LEU P 4 " pdb=" N LEU P 4 " pdb=" C LEU P 4 " pdb=" CB LEU P 4 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 1479 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.117 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO P 32 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO N 100 " -0.009 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C PRO N 100 " 0.034 2.00e-02 2.50e+03 pdb=" O PRO N 100 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA N 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.018 2.00e-02 2.50e+03 1.19e-02 3.54e+00 pdb=" CG TRP A 234 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.001 2.00e-02 2.50e+03 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2612 2.80 - 3.32: 8594 3.32 - 3.85: 15104 3.85 - 4.37: 18671 4.37 - 4.90: 31288 Nonbonded interactions: 76269 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.306 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.315 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.321 2.440 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.328 2.440 ... (remaining 76264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.000 Extract box with map and model: 6.650 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.340 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 0.053 9700 Z= 0.204 Angle : 0.605 11.790 13179 Z= 0.407 Chirality : 0.043 0.204 1482 Planarity : 0.005 0.167 1699 Dihedral : 12.285 89.913 3375 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -4.28 (0.19), residues: 1226 helix: -3.18 (0.18), residues: 442 sheet: -3.15 (0.31), residues: 197 loop : -2.32 (0.22), residues: 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 200 average time/residue: 0.2419 time to fit residues: 65.5717 Evaluate side-chains 151 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1042 time to fit residues: 2.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 8.9990 chunk 90 optimal weight: 0.0270 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 230 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN E 124 HIS P 17 ASN R 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9700 Z= 0.161 Angle : 0.471 6.433 13179 Z= 0.251 Chirality : 0.040 0.151 1482 Planarity : 0.004 0.054 1699 Dihedral : 3.553 13.803 1344 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 1.57 % 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: -2.88 (0.21), residues: 1226 helix: -1.48 (0.22), residues: 466 sheet: -2.39 (0.32), residues: 223 loop : -1.94 (0.23), residues: 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.180 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 176 average time/residue: 0.2471 time to fit residues: 60.2671 Evaluate side-chains 150 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0949 time to fit residues: 2.8088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9700 Z= 0.200 Angle : 0.484 7.294 13179 Z= 0.255 Chirality : 0.041 0.153 1482 Planarity : 0.004 0.045 1699 Dihedral : 3.755 16.249 1344 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 2.30 % 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: -2.22 (0.22), residues: 1226 helix: -0.68 (0.23), residues: 470 sheet: -2.28 (0.31), residues: 230 loop : -1.69 (0.24), residues: 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.123 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 166 average time/residue: 0.2130 time to fit residues: 49.7092 Evaluate side-chains 150 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0916 time to fit residues: 3.6120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9700 Z= 0.162 Angle : 0.459 7.948 13179 Z= 0.243 Chirality : 0.041 0.161 1482 Planarity : 0.003 0.045 1699 Dihedral : 3.656 16.239 1344 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.99 % 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: -1.76 (0.23), residues: 1226 helix: -0.18 (0.24), residues: 471 sheet: -2.12 (0.32), residues: 225 loop : -1.53 (0.24), residues: 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.021 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 161 average time/residue: 0.2108 time to fit residues: 47.7861 Evaluate side-chains 147 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0910 time to fit residues: 2.9319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 23 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9700 Z= 0.166 Angle : 0.459 8.016 13179 Z= 0.241 Chirality : 0.040 0.149 1482 Planarity : 0.003 0.044 1699 Dihedral : 3.633 16.404 1344 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.26 % 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: -1.48 (0.23), residues: 1226 helix: 0.16 (0.25), residues: 471 sheet: -2.08 (0.31), residues: 230 loop : -1.42 (0.25), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.002 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 153 average time/residue: 0.2235 time to fit residues: 48.5344 Evaluate side-chains 144 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0926 time to fit residues: 2.8270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9700 Z= 0.234 Angle : 0.506 8.579 13179 Z= 0.264 Chirality : 0.042 0.147 1482 Planarity : 0.003 0.046 1699 Dihedral : 3.960 17.979 1344 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.36 % 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: -1.43 (0.23), residues: 1226 helix: 0.21 (0.25), residues: 472 sheet: -2.05 (0.31), residues: 231 loop : -1.40 (0.25), residues: 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.109 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 0.2178 time to fit residues: 42.6352 Evaluate side-chains 134 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0979 time to fit residues: 3.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN N 13 GLN N 31 ASN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9700 Z= 0.242 Angle : 0.513 7.956 13179 Z= 0.269 Chirality : 0.042 0.162 1482 Planarity : 0.003 0.047 1699 Dihedral : 4.066 17.908 1344 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.73 % 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: -1.39 (0.23), residues: 1226 helix: 0.34 (0.25), residues: 466 sheet: -2.05 (0.31), residues: 221 loop : -1.47 (0.24), residues: 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.101 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 133 average time/residue: 0.2288 time to fit residues: 42.9084 Evaluate side-chains 132 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0970 time to fit residues: 2.4188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 0.0070 chunk 105 optimal weight: 0.0020 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 9700 Z= 0.120 Angle : 0.456 7.502 13179 Z= 0.241 Chirality : 0.040 0.273 1482 Planarity : 0.003 0.045 1699 Dihedral : 3.605 20.698 1344 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.84 % 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: -1.06 (0.24), residues: 1226 helix: 0.68 (0.26), residues: 471 sheet: -1.96 (0.31), residues: 220 loop : -1.32 (0.25), residues: 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.126 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.2276 time to fit residues: 48.5500 Evaluate side-chains 135 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0986 time to fit residues: 2.2424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN N 31 ASN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 9700 Z= 0.138 Angle : 0.463 8.389 13179 Z= 0.242 Chirality : 0.040 0.267 1482 Planarity : 0.003 0.045 1699 Dihedral : 3.575 19.506 1344 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.42 % 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 (0.24), residues: 1226 helix: 0.80 (0.26), residues: 469 sheet: -1.89 (0.32), residues: 220 loop : -1.26 (0.25), residues: 537 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.201 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 140 average time/residue: 0.2207 time to fit residues: 43.8535 Evaluate side-chains 136 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1010 time to fit residues: 2.1305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.0980 chunk 119 optimal weight: 0.2980 chunk 110 optimal weight: 0.0670 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 0.0170 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 9700 Z= 0.117 Angle : 0.454 9.626 13179 Z= 0.237 Chirality : 0.040 0.257 1482 Planarity : 0.003 0.042 1699 Dihedral : 3.426 20.073 1344 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.10 % 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: -0.71 (0.24), residues: 1226 helix: 1.01 (0.26), residues: 469 sheet: -1.83 (0.32), residues: 222 loop : -1.13 (0.25), residues: 535 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.725 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.2219 time to fit residues: 42.8812 Evaluate side-chains 130 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0050 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 97 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.200989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.169275 restraints weight = 10678.772| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.85 r_work: 0.3721 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 9700 Z= 0.123 Angle : 0.465 11.851 13179 Z= 0.240 Chirality : 0.040 0.246 1482 Planarity : 0.003 0.042 1699 Dihedral : 3.402 19.626 1344 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -0.62 (0.24), residues: 1226 helix: 1.10 (0.26), residues: 469 sheet: -1.79 (0.32), residues: 224 loop : -1.09 (0.25), residues: 533 =============================================================================== Job complete usr+sys time: 2275.92 seconds wall clock time: 42 minutes 2.73 seconds (2522.73 seconds total)