Starting phenix.real_space_refine on Wed Feb 14 08:37:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/02_2024/7lll_23425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/02_2024/7lll_23425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/02_2024/7lll_23425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/02_2024/7lll_23425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/02_2024/7lll_23425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lll_23425/02_2024/7lll_23425.pdb" } resolution = 3.7 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= 0.004 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 56 5.16 5 C 5670 2.51 5 N 1555 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8940 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2615 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "R" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2749 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 13, 'TRANS': 352} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 210 Time building chain proxies: 4.70, per 1000 atoms: 0.53 Number of scatterers: 8940 At special positions: 0 Unit cell: (87.87, 103.53, 174, 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 56 16.00 O 1659 8.00 N 1555 7.00 C 5670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.05 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 13 sheets defined 38.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.772A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.601A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.785A pdb=" N LYS A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.659A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.785A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.655A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.705A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 380 through 391 removed outlier: 3.833A pdb=" N MET A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 23 removed outlier: 4.258A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.699A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 21 removed outlier: 3.854A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 34 through 44 removed outlier: 4.228A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.815A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.182A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 removed outlier: 4.144A pdb=" N SER P 8 " --> pdb=" O GLY P 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA P 18 " --> pdb=" O MET P 14 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL P 19 " --> pdb=" O GLU P 15 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP P 25 " --> pdb=" O LEU P 21 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU P 26 " --> pdb=" O PHE P 22 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS P 27 " --> pdb=" O ILE P 23 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN P 28 " --> pdb=" O GLU P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.720A pdb=" N VAL R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS R 46 " --> pdb=" O TYR R 42 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 Processing helix chain 'R' and resid 139 through 149 removed outlier: 4.164A pdb=" N TYR R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 169 removed outlier: 3.801A pdb=" N LEU R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 156 " --> pdb=" O TYR R 152 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 204 removed outlier: 3.822A pdb=" N HIS R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN R 182 " --> pdb=" O TYR R 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 189 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA R 199 " --> pdb=" O PHE R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 removed outlier: 4.235A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 237 removed outlier: 3.983A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 251 Processing helix chain 'R' and resid 264 through 268 Processing helix chain 'R' and resid 269 through 274 removed outlier: 3.500A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 280 Processing helix chain 'R' and resid 281 through 291 removed outlier: 3.603A pdb=" N VAL R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.817A pdb=" N THR R 298 " --> pdb=" O GLY R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 308 Processing helix chain 'R' and resid 310 through 329 removed outlier: 3.509A pdb=" N PHE R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE R 324 " --> pdb=" O ASN R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 338 removed outlier: 3.765A pdb=" N LEU R 335 " --> pdb=" O VAL R 331 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 361 removed outlier: 3.866A pdb=" N THR R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 378 through 391 removed outlier: 3.839A pdb=" N THR R 386 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 404 removed outlier: 3.538A pdb=" N PHE R 404 " --> pdb=" O ILE R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 removed outlier: 3.693A pdb=" N ARG R 414 " --> pdb=" O GLN R 410 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.815A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 245 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.526A pdb=" N TYR B 59 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.640A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.663A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.029A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.638A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.841A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 295 through 297 removed outlier: 6.655A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320 removed outlier: 4.077A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 329 " --> pdb=" O LYS B 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'N' and resid 45 through 51 removed outlier: 6.708A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 73 removed outlier: 3.770A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 80 through 81 removed outlier: 4.039A pdb=" N VAL R 81 " --> pdb=" O ARG R 102 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 269 hydrogen bonds defined for protein. 753 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: 2.12 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 1817 1.45 - 1.58: 4870 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9120 Sorted by residual: bond pdb=" N VAL R 370 " pdb=" CA VAL R 370 " ideal model delta sigma weight residual 1.460 1.493 -0.033 8.60e-03 1.35e+04 1.47e+01 bond pdb=" C TRP R 72 " pdb=" N PRO R 73 " ideal model delta sigma weight residual 1.332 1.377 -0.045 1.26e-02 6.30e+03 1.30e+01 bond pdb=" C LEU R 311 " pdb=" N PRO R 312 " ideal model delta sigma weight residual 1.335 1.382 -0.046 1.36e-02 5.41e+03 1.17e+01 bond pdb=" N LEU R 359 " pdb=" CA LEU R 359 " ideal model delta sigma weight residual 1.458 1.500 -0.043 1.27e-02 6.20e+03 1.14e+01 bond pdb=" N GLU R 294 " pdb=" CA GLU R 294 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.23e-02 6.61e+03 9.75e+00 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.92: 190 106.92 - 113.77: 5017 113.77 - 120.62: 3819 120.62 - 127.47: 3244 127.47 - 134.32: 89 Bond angle restraints: 12359 Sorted by residual: angle pdb=" N VAL R 370 " pdb=" CA VAL R 370 " pdb=" C VAL R 370 " ideal model delta sigma weight residual 113.71 107.88 5.83 9.50e-01 1.11e+00 3.77e+01 angle pdb=" N PRO R 358 " pdb=" CA PRO R 358 " pdb=" C PRO R 358 " ideal model delta sigma weight residual 113.65 121.59 -7.94 1.35e+00 5.49e-01 3.46e+01 angle pdb=" C VAL R 281 " pdb=" N VAL R 282 " pdb=" CA VAL R 282 " ideal model delta sigma weight residual 120.33 125.01 -4.68 8.00e-01 1.56e+00 3.42e+01 angle pdb=" C TRP R 72 " pdb=" N PRO R 73 " pdb=" CA PRO R 73 " ideal model delta sigma weight residual 119.92 125.12 -5.20 1.07e+00 8.73e-01 2.36e+01 angle pdb=" N LEU R 268 " pdb=" CA LEU R 268 " pdb=" C LEU R 268 " ideal model delta sigma weight residual 112.41 106.10 6.31 1.30e+00 5.92e-01 2.36e+01 ... (remaining 12354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4911 17.84 - 35.68: 425 35.68 - 53.52: 65 53.52 - 71.36: 5 71.36 - 89.20: 8 Dihedral angle restraints: 5414 sinusoidal: 2061 harmonic: 3353 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 144.85 -51.85 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CA PHE R 230 " pdb=" C PHE R 230 " pdb=" N LEU R 231 " pdb=" CA LEU R 231 " ideal model delta harmonic sigma weight residual 180.00 151.90 28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA TYR R 291 " pdb=" C TYR R 291 " pdb=" N GLU R 292 " pdb=" CA GLU R 292 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1150 0.068 - 0.136: 206 0.136 - 0.203: 27 0.203 - 0.271: 4 0.271 - 0.339: 2 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA PRO R 358 " pdb=" N PRO R 358 " pdb=" C PRO R 358 " pdb=" CB PRO R 358 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA MET R 303 " pdb=" N MET R 303 " pdb=" C MET R 303 " pdb=" CB MET R 303 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PHE R 280 " pdb=" N PHE R 280 " pdb=" C PHE R 280 " pdb=" CB PHE R 280 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1386 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 383 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C LYS R 383 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS R 383 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU R 384 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO G 55 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 294 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C GLU R 294 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU R 294 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY R 295 " -0.015 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 227 2.68 - 3.23: 8467 3.23 - 3.79: 11765 3.79 - 4.34: 16467 4.34 - 4.90: 27069 Nonbonded interactions: 63995 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.124 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.165 2.440 nonbonded pdb=" OG1 THR A 369 " pdb=" OD1 ASN A 371 " model vdw 2.185 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.199 2.440 ... (remaining 63990 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 4.190 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.740 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.006 0.046 9120 Z= 0.382 Angle : 0.901 11.826 12359 Z= 0.591 Chirality : 0.055 0.339 1389 Planarity : 0.005 0.097 1580 Dihedral : 13.684 89.195 3224 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.11 % Allowed : 2.05 % Favored : 97.84 % 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: -4.22 (0.22), residues: 1129 helix: -2.86 (0.23), residues: 382 sheet: -3.15 (0.34), residues: 188 loop : -2.55 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS G 44 PHE 0.026 0.002 PHE N 108 TYR 0.011 0.001 TYR A 360 ARG 0.007 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.004 Fit side-chains REVERT: A 14 ASN cc_start: 0.7611 (m110) cc_final: 0.7407 (m110) REVERT: R 204 MET cc_start: 0.5246 (ttt) cc_final: 0.4968 (tmm) REVERT: R 224 LEU cc_start: 0.8116 (tp) cc_final: 0.7749 (mm) REVERT: R 267 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7670 (ptm160) REVERT: R 351 LYS cc_start: 0.7412 (tptt) cc_final: 0.6745 (tttm) REVERT: R 371 MET cc_start: 0.6187 (ppp) cc_final: 0.5239 (ppp) REVERT: R 414 ARG cc_start: 0.7097 (tpp-160) cc_final: 0.6026 (ttm110) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2503 time to fit residues: 54.0287 Evaluate side-chains 127 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 40.0000 chunk 47 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9120 Z= 0.161 Angle : 0.600 10.938 12359 Z= 0.319 Chirality : 0.042 0.164 1389 Planarity : 0.005 0.073 1580 Dihedral : 5.205 24.162 1247 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.97 % Allowed : 8.32 % Favored : 90.71 % 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: -3.68 (0.22), residues: 1129 helix: -2.17 (0.23), residues: 408 sheet: -2.69 (0.34), residues: 197 loop : -2.46 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.011 0.001 HIS R 171 PHE 0.019 0.002 PHE R 280 TYR 0.014 0.001 TYR R 291 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.070 Fit side-chains REVERT: A 31 GLN cc_start: 0.7817 (mm110) cc_final: 0.7509 (tp40) REVERT: B 59 TYR cc_start: 0.8758 (m-80) cc_final: 0.8475 (m-80) REVERT: R 345 ILE cc_start: 0.6811 (mm) cc_final: 0.6582 (mt) REVERT: R 351 LYS cc_start: 0.7253 (tptt) cc_final: 0.6827 (tttt) REVERT: R 371 MET cc_start: 0.6145 (ppp) cc_final: 0.5287 (ppp) REVERT: R 410 GLN cc_start: 0.6768 (mt0) cc_final: 0.6551 (mm-40) REVERT: R 414 ARG cc_start: 0.6752 (tpp-160) cc_final: 0.5963 (ttm110) outliers start: 9 outliers final: 6 residues processed: 143 average time/residue: 0.2409 time to fit residues: 46.4047 Evaluate side-chains 129 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 50.0000 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 50.0000 chunk 100 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9120 Z= 0.181 Angle : 0.579 11.066 12359 Z= 0.303 Chirality : 0.041 0.164 1389 Planarity : 0.004 0.059 1580 Dihedral : 4.920 23.052 1247 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.08 % Allowed : 11.66 % Favored : 87.26 % 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: -3.18 (0.23), residues: 1129 helix: -1.66 (0.25), residues: 407 sheet: -2.40 (0.35), residues: 194 loop : -2.27 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.004 0.001 HIS R 171 PHE 0.028 0.002 PHE R 280 TYR 0.016 0.001 TYR R 291 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.097 Fit side-chains REVERT: B 217 MET cc_start: 0.7952 (ttm) cc_final: 0.7743 (mmm) REVERT: R 230 PHE cc_start: 0.7138 (m-10) cc_final: 0.6301 (t80) REVERT: R 345 ILE cc_start: 0.6743 (mm) cc_final: 0.6484 (mt) REVERT: R 351 LYS cc_start: 0.7431 (tptt) cc_final: 0.6708 (tttt) REVERT: R 371 MET cc_start: 0.6370 (ppp) cc_final: 0.5376 (ppp) REVERT: R 414 ARG cc_start: 0.6796 (tpp-160) cc_final: 0.6021 (ttm110) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.2395 time to fit residues: 42.7960 Evaluate side-chains 124 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9120 Z= 0.180 Angle : 0.567 11.224 12359 Z= 0.295 Chirality : 0.041 0.164 1389 Planarity : 0.004 0.055 1580 Dihedral : 4.754 22.747 1247 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.27 % Allowed : 12.42 % Favored : 85.31 % 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: -2.94 (0.24), residues: 1129 helix: -1.42 (0.25), residues: 409 sheet: -2.25 (0.36), residues: 198 loop : -2.18 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 297 HIS 0.003 0.001 HIS G 44 PHE 0.016 0.001 PHE N 108 TYR 0.017 0.001 TYR R 291 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.944 Fit side-chains REVERT: R 230 PHE cc_start: 0.7107 (m-10) cc_final: 0.6268 (t80) REVERT: R 345 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6188 (tp) REVERT: R 351 LYS cc_start: 0.7432 (tptt) cc_final: 0.6367 (tttt) REVERT: R 371 MET cc_start: 0.6488 (ppp) cc_final: 0.5454 (ppp) REVERT: R 414 ARG cc_start: 0.6681 (tpp-160) cc_final: 0.5922 (ttm110) outliers start: 21 outliers final: 11 residues processed: 134 average time/residue: 0.2285 time to fit residues: 41.5917 Evaluate side-chains 127 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.0570 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9120 Z= 0.166 Angle : 0.547 11.231 12359 Z= 0.283 Chirality : 0.040 0.161 1389 Planarity : 0.004 0.052 1580 Dihedral : 4.547 22.004 1247 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.27 % Allowed : 14.58 % Favored : 83.15 % 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: -2.73 (0.24), residues: 1129 helix: -1.16 (0.25), residues: 415 sheet: -2.09 (0.36), residues: 195 loop : -2.16 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 297 HIS 0.003 0.001 HIS G 44 PHE 0.015 0.001 PHE N 108 TYR 0.017 0.001 TYR R 291 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.021 Fit side-chains REVERT: A 314 GLU cc_start: 0.6390 (tm-30) cc_final: 0.6042 (tm-30) REVERT: B 129 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7277 (ttp80) REVERT: R 230 PHE cc_start: 0.7068 (m-10) cc_final: 0.6228 (t80) REVERT: R 345 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6234 (tp) outliers start: 21 outliers final: 13 residues processed: 131 average time/residue: 0.2445 time to fit residues: 43.3600 Evaluate side-chains 120 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9120 Z= 0.138 Angle : 0.525 11.714 12359 Z= 0.270 Chirality : 0.040 0.158 1389 Planarity : 0.003 0.050 1580 Dihedral : 4.282 21.548 1247 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.73 % Allowed : 15.55 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.24), residues: 1129 helix: -0.86 (0.26), residues: 417 sheet: -1.87 (0.36), residues: 200 loop : -2.02 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS G 44 PHE 0.018 0.001 PHE R 280 TYR 0.015 0.001 TYR R 291 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.054 Fit side-chains REVERT: A 314 GLU cc_start: 0.6364 (tm-30) cc_final: 0.6034 (tm-30) REVERT: B 17 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7444 (tt0) REVERT: B 129 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7251 (ttp80) REVERT: N 105 ARG cc_start: 0.6404 (ttm-80) cc_final: 0.6188 (ttm170) REVERT: R 230 PHE cc_start: 0.6958 (m-10) cc_final: 0.6247 (t80) REVERT: R 303 MET cc_start: 0.7155 (tpp) cc_final: 0.6931 (tpp) REVERT: R 345 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.5968 (tp) REVERT: R 371 MET cc_start: 0.6583 (ppp) cc_final: 0.5246 (ppp) outliers start: 16 outliers final: 10 residues processed: 123 average time/residue: 0.2202 time to fit residues: 37.5202 Evaluate side-chains 116 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0170 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 50.0000 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9120 Z= 0.168 Angle : 0.542 12.433 12359 Z= 0.280 Chirality : 0.040 0.160 1389 Planarity : 0.003 0.050 1580 Dihedral : 4.347 20.991 1247 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.16 % Allowed : 16.52 % Favored : 81.32 % 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: -2.21 (0.25), residues: 1129 helix: -0.66 (0.26), residues: 414 sheet: -1.80 (0.36), residues: 200 loop : -1.95 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 297 HIS 0.003 0.001 HIS G 44 PHE 0.017 0.001 PHE R 280 TYR 0.015 0.001 TYR R 291 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.976 Fit side-chains REVERT: A 314 GLU cc_start: 0.6374 (tm-30) cc_final: 0.6038 (tm-30) REVERT: B 17 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7469 (tt0) REVERT: B 129 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7266 (ttp80) REVERT: R 230 PHE cc_start: 0.6979 (m-10) cc_final: 0.6258 (t80) REVERT: R 303 MET cc_start: 0.7128 (tpp) cc_final: 0.6875 (tpp) REVERT: R 345 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.5983 (tp) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.2235 time to fit residues: 37.3440 Evaluate side-chains 121 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.0170 chunk 103 optimal weight: 3.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9120 Z= 0.122 Angle : 0.504 11.279 12359 Z= 0.259 Chirality : 0.039 0.165 1389 Planarity : 0.003 0.049 1580 Dihedral : 3.958 20.473 1247 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 16.52 % Favored : 81.64 % 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: -1.86 (0.25), residues: 1129 helix: -0.31 (0.27), residues: 410 sheet: -1.35 (0.36), residues: 199 loop : -1.91 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.001 0.000 HIS A 362 PHE 0.017 0.001 PHE R 280 TYR 0.015 0.001 TYR R 291 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.969 Fit side-chains REVERT: A 314 GLU cc_start: 0.6323 (tm-30) cc_final: 0.6019 (tm-30) REVERT: B 17 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7473 (tt0) REVERT: B 129 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7220 (ttp80) REVERT: N 63 SER cc_start: 0.8365 (m) cc_final: 0.7935 (t) REVERT: R 230 PHE cc_start: 0.6824 (m-10) cc_final: 0.6273 (t80) REVERT: R 345 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5822 (tp) REVERT: R 371 MET cc_start: 0.6525 (ppp) cc_final: 0.5174 (ppp) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.2169 time to fit residues: 37.5030 Evaluate side-chains 121 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9120 Z= 0.162 Angle : 0.534 10.873 12359 Z= 0.276 Chirality : 0.040 0.184 1389 Planarity : 0.003 0.049 1580 Dihedral : 4.098 15.844 1247 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.73 % Allowed : 17.06 % Favored : 81.21 % 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: -1.77 (0.25), residues: 1129 helix: -0.21 (0.27), residues: 415 sheet: -1.36 (0.35), residues: 210 loop : -1.86 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 297 HIS 0.003 0.001 HIS G 44 PHE 0.016 0.001 PHE R 280 TYR 0.014 0.001 TYR R 291 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.920 Fit side-chains REVERT: A 314 GLU cc_start: 0.6330 (tm-30) cc_final: 0.6021 (tm-30) REVERT: B 17 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7472 (tt0) REVERT: B 129 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7265 (ttp80) REVERT: R 230 PHE cc_start: 0.6802 (m-10) cc_final: 0.6260 (t80) REVERT: R 345 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5866 (tp) outliers start: 16 outliers final: 12 residues processed: 111 average time/residue: 0.2154 time to fit residues: 32.8474 Evaluate side-chains 113 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9120 Z= 0.130 Angle : 0.510 10.244 12359 Z= 0.264 Chirality : 0.039 0.159 1389 Planarity : 0.003 0.049 1580 Dihedral : 3.940 15.285 1247 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.40 % Allowed : 17.60 % Favored : 80.99 % 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: -1.57 (0.25), residues: 1129 helix: -0.04 (0.27), residues: 414 sheet: -1.27 (0.35), residues: 211 loop : -1.74 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 297 HIS 0.002 0.000 HIS G 44 PHE 0.017 0.001 PHE R 280 TYR 0.014 0.001 TYR R 291 ARG 0.004 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.947 Fit side-chains REVERT: A 314 GLU cc_start: 0.6330 (tm-30) cc_final: 0.6015 (tm-30) REVERT: B 17 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7487 (tt0) REVERT: B 129 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7223 (ttp80) REVERT: N 63 SER cc_start: 0.8389 (m) cc_final: 0.7960 (t) REVERT: P 22 PHE cc_start: 0.7702 (t80) cc_final: 0.7183 (m-10) REVERT: R 230 PHE cc_start: 0.6721 (m-10) cc_final: 0.6264 (t80) REVERT: R 345 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5821 (tp) outliers start: 13 outliers final: 12 residues processed: 111 average time/residue: 0.2299 time to fit residues: 35.2199 Evaluate side-chains 116 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139201 restraints weight = 10347.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133909 restraints weight = 21080.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134521 restraints weight = 23092.626| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9120 Z= 0.179 Angle : 0.549 10.425 12359 Z= 0.283 Chirality : 0.041 0.157 1389 Planarity : 0.003 0.049 1580 Dihedral : 4.162 15.648 1247 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.84 % Allowed : 17.28 % Favored : 80.89 % 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: -1.63 (0.25), residues: 1129 helix: -0.04 (0.27), residues: 417 sheet: -1.39 (0.35), residues: 213 loop : -1.78 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 297 HIS 0.003 0.001 HIS G 44 PHE 0.017 0.001 PHE R 280 TYR 0.014 0.001 TYR R 291 ARG 0.003 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.86 seconds wall clock time: 35 minutes 32.30 seconds (2132.30 seconds total)