Starting phenix.real_space_refine on Fri Sep 27 05:49:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/09_2024/7to3_26028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/09_2024/7to3_26028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/09_2024/7to3_26028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/09_2024/7to3_26028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/09_2024/7to3_26028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to3_26028/09_2024/7to3_26028.cif" } resolution = 2.74 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= 0.010 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 44 5.16 5 C 9346 2.51 5 N 2572 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14764 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4421 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2878 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 83 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Restraints were copied for chains: D, B Time building chain proxies: 14.60, per 1000 atoms: 0.99 Number of scatterers: 14764 At special positions: 0 Unit cell: (147, 126.84, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 12 15.00 Mg 4 11.99 O 2786 8.00 N 2572 7.00 C 9346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.9 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 12 sheets defined 40.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.624A pdb=" N TRP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.552A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.694A pdb=" N SER A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 4.150A pdb=" N HIS A 421 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.538A pdb=" N LEU A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.915A pdb=" N ALA A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 577 Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 128 through 150 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.624A pdb=" N TRP B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.552A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.693A pdb=" N SER B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 4.149A pdb=" N HIS B 421 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 479 through 488 removed outlier: 3.538A pdb=" N LEU B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.916A pdb=" N ALA B 524 " --> pdb=" O PRO B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 577 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 206 through 221 removed outlier: 4.029A pdb=" N GLN C 210 " --> pdb=" O HIS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.605A pdb=" N ALA C 306 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG C 307 " --> pdb=" O VAL C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 307' Processing helix chain 'C' and resid 309 through 333 removed outlier: 3.556A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.960A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 Processing helix chain 'D' and resid 17 through 38 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 206 through 221 removed outlier: 4.030A pdb=" N GLN D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 266 through 282 Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.606A pdb=" N ALA D 306 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG D 307 " --> pdb=" O VAL D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 307' Processing helix chain 'D' and resid 309 through 333 removed outlier: 3.556A pdb=" N ALA D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.961A pdb=" N LEU D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.746A pdb=" N ARG A 221 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE A 212 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 194 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR A 236 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N LEU A 294 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN A 237 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU A 296 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 239 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY A 298 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER A 241 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 311 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N ILE A 312 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN A 360 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TRP A 314 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR A 358 " --> pdb=" O TRP A 314 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 316 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP A 355 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG A 357 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 171 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLN A 359 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 173 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU A 207 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 172 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 209 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY A 174 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLU A 211 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 452 removed outlier: 6.519A pdb=" N GLN A 405 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE A 452 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 407 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.746A pdb=" N ARG B 221 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N LEU B 294 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASN B 237 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 296 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 239 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY B 298 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER B 241 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N ILE B 312 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASN B 360 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TRP B 314 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR B 358 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 316 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TRP B 355 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG B 357 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 171 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLN B 359 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 173 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 207 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 172 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU B 209 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY B 174 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU B 211 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 448 through 452 removed outlier: 6.518A pdb=" N GLN B 405 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE B 452 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 407 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 51 removed outlier: 6.584A pdb=" N VAL C 75 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 48 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 73 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU C 50 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP C 71 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL C 70 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 123 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 72 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR C 125 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 74 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 192 through 195 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 51 removed outlier: 6.583A pdb=" N VAL D 75 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR D 48 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 73 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU D 50 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP D 71 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 70 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL D 123 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 72 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR D 125 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 74 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 192 through 195 626 hydrogen bonds defined for protein. 1788 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: 4.73 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4847 1.35 - 1.46: 3467 1.46 - 1.58: 6746 1.58 - 1.69: 18 1.69 - 1.81: 72 Bond restraints: 15150 Sorted by residual: bond pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.75e+00 bond pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 1.528 1.549 -0.021 1.59e-02 3.96e+03 1.68e+00 bond pdb=" C GLU B 69 " pdb=" O GLU B 69 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.24e-02 6.50e+03 9.88e-01 bond pdb=" C4 ADP D 405 " pdb=" C5 ADP D 405 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.57e-01 bond pdb=" C4 AMP D 401 " pdb=" C5 AMP D 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.50e-01 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 19942 1.19 - 2.38: 504 2.38 - 3.57: 138 3.57 - 4.76: 42 4.76 - 5.95: 28 Bond angle restraints: 20654 Sorted by residual: angle pdb=" N ILE B 220 " pdb=" CA ILE B 220 " pdb=" C ILE B 220 " ideal model delta sigma weight residual 113.71 110.28 3.43 9.50e-01 1.11e+00 1.31e+01 angle pdb=" N ILE A 220 " pdb=" CA ILE A 220 " pdb=" C ILE A 220 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N TRP C 24 " pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " ideal model delta sigma weight residual 110.16 115.00 -4.84 1.48e+00 4.57e-01 1.07e+01 angle pdb=" N TRP D 24 " pdb=" CA TRP D 24 " pdb=" CB TRP D 24 " ideal model delta sigma weight residual 110.16 114.93 -4.77 1.48e+00 4.57e-01 1.04e+01 angle pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " pdb=" CG TRP C 24 " ideal model delta sigma weight residual 113.60 119.55 -5.95 1.90e+00 2.77e-01 9.81e+00 ... (remaining 20649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 8900 34.13 - 68.26: 124 68.26 - 102.39: 2 102.39 - 136.51: 2 136.51 - 170.64: 4 Dihedral angle restraints: 9032 sinusoidal: 3670 harmonic: 5362 Sorted by residual: dihedral pdb=" O2A ADP D 405 " pdb=" O3A ADP D 405 " pdb=" PA ADP D 405 " pdb=" PB ADP D 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.36 170.64 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 129.37 170.63 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 148.68 151.32 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 9029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1643 0.033 - 0.067: 426 0.067 - 0.100: 119 0.100 - 0.133: 54 0.133 - 0.167: 8 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2247 not shown) Planarity restraints: 2648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 24 " -0.034 2.00e-02 2.50e+03 3.68e-02 3.38e+01 pdb=" CG TRP D 24 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP D 24 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP D 24 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 24 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 24 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 24 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 24 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 24 " 0.034 2.00e-02 2.50e+03 3.67e-02 3.36e+01 pdb=" CG TRP C 24 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP C 24 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 24 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 24 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 24 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 24 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 24 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 24 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 24 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 50 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 2645 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 34 2.63 - 3.20: 12066 3.20 - 3.76: 22019 3.76 - 4.33: 31687 4.33 - 4.90: 51683 Nonbonded interactions: 117489 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 2.062 2.170 nonbonded pdb="MG MG D 403 " pdb=" O2B ATP D 404 " model vdw 2.062 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 2.079 2.170 nonbonded pdb=" OD2 ASP D 69 " pdb="MG MG D 402 " model vdw 2.080 2.170 nonbonded pdb=" O ALA C 132 " pdb=" ND1 HIS C 136 " model vdw 2.317 3.120 ... (remaining 117484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.590 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: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.260 Find NCS groups from input model: 0.650 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15150 Z= 0.134 Angle : 0.544 5.950 20654 Z= 0.281 Chirality : 0.037 0.167 2250 Planarity : 0.004 0.049 2648 Dihedral : 12.122 170.644 5540 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.85 (0.19), residues: 1830 helix: 2.69 (0.20), residues: 664 sheet: 0.57 (0.27), residues: 348 loop : -1.32 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 PHE 0.011 0.001 PHE A 510 TYR 0.009 0.001 TYR D 225 ARG 0.001 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8130 (mt0) cc_final: 0.7499 (mm-40) REVERT: B 37 LYS cc_start: 0.9103 (mttt) cc_final: 0.8877 (tmmm) REVERT: B 39 TRP cc_start: 0.7299 (m100) cc_final: 0.6744 (m100) REVERT: B 414 GLN cc_start: 0.8084 (mt0) cc_final: 0.7459 (mm-40) REVERT: C 90 ASP cc_start: 0.8213 (m-30) cc_final: 0.8006 (m-30) REVERT: C 242 ASP cc_start: 0.8406 (m-30) cc_final: 0.7928 (t0) REVERT: D 242 ASP cc_start: 0.8403 (m-30) cc_final: 0.7938 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 1.6476 time to fit residues: 463.7743 Evaluate side-chains 110 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN B 94 ASN C 8 ASN C 210 GLN C 254 HIS D 8 ASN D 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15150 Z= 0.247 Angle : 0.599 7.099 20654 Z= 0.292 Chirality : 0.041 0.179 2250 Planarity : 0.005 0.057 2648 Dihedral : 9.748 146.790 2088 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 7.88 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.78 (0.19), residues: 1830 helix: 2.43 (0.20), residues: 674 sheet: 0.45 (0.27), residues: 336 loop : -1.16 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 24 HIS 0.010 0.001 HIS C 206 PHE 0.015 0.002 PHE C 10 TYR 0.018 0.002 TYR D 286 ARG 0.008 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7299 (m-40) REVERT: A 414 GLN cc_start: 0.8193 (mt0) cc_final: 0.7480 (mm-40) REVERT: B 39 TRP cc_start: 0.7587 (m100) cc_final: 0.6910 (m100) REVERT: B 215 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7351 (m-40) REVERT: B 414 GLN cc_start: 0.8138 (mt0) cc_final: 0.7391 (mm-40) REVERT: C 82 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8136 (mtp85) REVERT: C 90 ASP cc_start: 0.8134 (m-30) cc_final: 0.7874 (m-30) REVERT: C 162 LYS cc_start: 0.8876 (pttt) cc_final: 0.8172 (tppt) REVERT: C 242 ASP cc_start: 0.8426 (m-30) cc_final: 0.7869 (t0) REVERT: D 90 ASP cc_start: 0.8177 (m-30) cc_final: 0.7904 (m-30) REVERT: D 162 LYS cc_start: 0.8798 (pttt) cc_final: 0.8205 (tppt) REVERT: D 242 ASP cc_start: 0.8401 (m-30) cc_final: 0.7855 (t0) outliers start: 23 outliers final: 6 residues processed: 134 average time/residue: 1.4047 time to fit residues: 206.5398 Evaluate side-chains 93 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 0.0270 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 417 ASN C 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15150 Z= 0.294 Angle : 0.610 7.750 20654 Z= 0.295 Chirality : 0.042 0.174 2250 Planarity : 0.005 0.047 2648 Dihedral : 8.801 138.312 2088 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 9.50 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.75 (0.20), residues: 1830 helix: 2.32 (0.20), residues: 674 sheet: 0.58 (0.27), residues: 354 loop : -1.19 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 24 HIS 0.011 0.001 HIS C 206 PHE 0.018 0.002 PHE C 10 TYR 0.021 0.002 TYR D 286 ARG 0.008 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7406 (m-40) REVERT: A 414 GLN cc_start: 0.8190 (mt0) cc_final: 0.7420 (mm-40) REVERT: B 215 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7453 (m-40) REVERT: B 414 GLN cc_start: 0.8165 (mt0) cc_final: 0.7375 (mm-40) REVERT: C 90 ASP cc_start: 0.8122 (m-30) cc_final: 0.7860 (m-30) REVERT: C 162 LYS cc_start: 0.8828 (pttt) cc_final: 0.8209 (tppt) REVERT: C 242 ASP cc_start: 0.8469 (m-30) cc_final: 0.7835 (t0) REVERT: C 245 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8573 (tptp) REVERT: D 90 ASP cc_start: 0.8182 (m-30) cc_final: 0.7866 (m-30) REVERT: D 162 LYS cc_start: 0.8751 (pttt) cc_final: 0.8190 (tppt) REVERT: D 242 ASP cc_start: 0.8435 (m-30) cc_final: 0.7816 (t0) REVERT: D 245 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8622 (tptp) REVERT: D 286 TYR cc_start: 0.9094 (t80) cc_final: 0.8890 (t80) outliers start: 29 outliers final: 3 residues processed: 116 average time/residue: 1.4076 time to fit residues: 180.1040 Evaluate side-chains 89 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 245 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15150 Z= 0.202 Angle : 0.559 7.713 20654 Z= 0.268 Chirality : 0.040 0.173 2250 Planarity : 0.004 0.040 2648 Dihedral : 8.226 124.475 2088 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.23 % Allowed : 10.34 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.87 (0.20), residues: 1830 helix: 2.37 (0.20), residues: 686 sheet: 0.70 (0.27), residues: 354 loop : -1.16 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 24 HIS 0.006 0.001 HIS C 206 PHE 0.014 0.001 PHE B 510 TYR 0.018 0.001 TYR C 286 ARG 0.011 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8107 (mt0) cc_final: 0.7363 (mm-40) REVERT: B 414 GLN cc_start: 0.8107 (mt0) cc_final: 0.7357 (mm-40) REVERT: C 90 ASP cc_start: 0.8076 (m-30) cc_final: 0.7785 (m-30) REVERT: C 162 LYS cc_start: 0.8811 (pttt) cc_final: 0.8207 (tppt) REVERT: C 242 ASP cc_start: 0.8446 (m-30) cc_final: 0.7835 (t0) REVERT: C 305 MET cc_start: 0.8716 (mpp) cc_final: 0.8422 (mpt) REVERT: D 90 ASP cc_start: 0.8182 (m-30) cc_final: 0.7815 (m-30) REVERT: D 162 LYS cc_start: 0.8723 (pttt) cc_final: 0.8232 (tppt) REVERT: D 242 ASP cc_start: 0.8415 (m-30) cc_final: 0.7819 (t0) outliers start: 19 outliers final: 4 residues processed: 99 average time/residue: 1.4127 time to fit residues: 153.7181 Evaluate side-chains 82 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 0.0050 chunk 44 optimal weight: 3.9990 overall best weight: 0.7754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15150 Z= 0.192 Angle : 0.555 7.466 20654 Z= 0.265 Chirality : 0.039 0.167 2250 Planarity : 0.004 0.037 2648 Dihedral : 8.000 111.093 2088 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.03 % Allowed : 11.76 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.96 (0.20), residues: 1830 helix: 2.45 (0.20), residues: 686 sheet: 0.76 (0.27), residues: 354 loop : -1.12 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS C 206 PHE 0.014 0.001 PHE A 510 TYR 0.020 0.002 TYR C 286 ARG 0.007 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8121 (mt0) cc_final: 0.7351 (mm-40) REVERT: B 414 GLN cc_start: 0.8111 (mt0) cc_final: 0.7363 (mm-40) REVERT: C 90 ASP cc_start: 0.8058 (m-30) cc_final: 0.7754 (m-30) REVERT: C 162 LYS cc_start: 0.8775 (pttt) cc_final: 0.8196 (tppt) REVERT: C 242 ASP cc_start: 0.8446 (m-30) cc_final: 0.7844 (t0) REVERT: D 90 ASP cc_start: 0.8162 (m-30) cc_final: 0.7774 (m-30) REVERT: D 162 LYS cc_start: 0.8719 (pttt) cc_final: 0.8236 (tppt) REVERT: D 242 ASP cc_start: 0.8414 (m-30) cc_final: 0.7822 (t0) REVERT: D 305 MET cc_start: 0.8688 (mpp) cc_final: 0.8407 (mpt) outliers start: 16 outliers final: 5 residues processed: 89 average time/residue: 1.4340 time to fit residues: 140.5274 Evaluate side-chains 80 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15150 Z= 0.192 Angle : 0.543 7.704 20654 Z= 0.259 Chirality : 0.039 0.166 2250 Planarity : 0.004 0.036 2648 Dihedral : 7.738 91.626 2088 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.29 % Allowed : 12.27 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.02 (0.20), residues: 1830 helix: 2.50 (0.20), residues: 686 sheet: 0.80 (0.27), residues: 354 loop : -1.11 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS D 206 PHE 0.014 0.001 PHE B 510 TYR 0.012 0.001 TYR C 250 ARG 0.007 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8159 (mt0) cc_final: 0.7401 (mm-40) REVERT: B 414 GLN cc_start: 0.8137 (mt0) cc_final: 0.7353 (mm-40) REVERT: C 90 ASP cc_start: 0.8086 (m-30) cc_final: 0.7767 (m-30) REVERT: C 162 LYS cc_start: 0.8746 (pttt) cc_final: 0.8165 (tppt) REVERT: C 242 ASP cc_start: 0.8438 (m-30) cc_final: 0.7842 (t0) REVERT: C 305 MET cc_start: 0.8694 (mpp) cc_final: 0.8398 (mpt) REVERT: D 90 ASP cc_start: 0.8142 (m-30) cc_final: 0.7753 (m-30) REVERT: D 162 LYS cc_start: 0.8699 (pttt) cc_final: 0.8242 (tppt) REVERT: D 242 ASP cc_start: 0.8411 (m-30) cc_final: 0.7824 (t0) REVERT: D 305 MET cc_start: 0.8644 (mpp) cc_final: 0.8242 (mpt) outliers start: 20 outliers final: 9 residues processed: 92 average time/residue: 1.4041 time to fit residues: 142.4199 Evaluate side-chains 80 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Chi-restraints excluded: chain D residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15150 Z= 0.254 Angle : 0.582 9.498 20654 Z= 0.281 Chirality : 0.041 0.168 2250 Planarity : 0.004 0.036 2648 Dihedral : 7.714 81.609 2088 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.03 % Allowed : 12.47 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.90 (0.20), residues: 1830 helix: 2.42 (0.20), residues: 686 sheet: 0.68 (0.27), residues: 358 loop : -1.17 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 24 HIS 0.006 0.001 HIS C 206 PHE 0.016 0.002 PHE D 10 TYR 0.014 0.002 TYR D 250 ARG 0.009 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8170 (mt0) cc_final: 0.7375 (mm-40) REVERT: B 414 GLN cc_start: 0.8173 (mt0) cc_final: 0.7378 (mm-40) REVERT: C 90 ASP cc_start: 0.8103 (m-30) cc_final: 0.7779 (m-30) REVERT: C 162 LYS cc_start: 0.8725 (pttt) cc_final: 0.8212 (tppt) REVERT: C 242 ASP cc_start: 0.8422 (m-30) cc_final: 0.7821 (t0) REVERT: C 305 MET cc_start: 0.8674 (mpp) cc_final: 0.8248 (mpt) REVERT: D 162 LYS cc_start: 0.8685 (pttt) cc_final: 0.8211 (tppt) REVERT: D 242 ASP cc_start: 0.8414 (m-30) cc_final: 0.7821 (t0) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 1.4185 time to fit residues: 139.4341 Evaluate side-chains 81 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15150 Z= 0.171 Angle : 0.543 10.452 20654 Z= 0.261 Chirality : 0.039 0.168 2250 Planarity : 0.004 0.033 2648 Dihedral : 7.491 71.767 2088 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.90 % Allowed : 12.79 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.07 (0.20), residues: 1830 helix: 2.57 (0.20), residues: 686 sheet: 0.79 (0.27), residues: 358 loop : -1.08 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 24 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.010 0.001 TYR C 250 ARG 0.009 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8150 (mt0) cc_final: 0.7398 (mm-40) REVERT: B 414 GLN cc_start: 0.8157 (mt0) cc_final: 0.7411 (mm-40) REVERT: C 90 ASP cc_start: 0.8078 (m-30) cc_final: 0.7779 (m-30) REVERT: C 162 LYS cc_start: 0.8691 (pttt) cc_final: 0.8177 (tppt) REVERT: C 242 ASP cc_start: 0.8408 (m-30) cc_final: 0.7832 (t0) REVERT: C 305 MET cc_start: 0.8659 (mpp) cc_final: 0.8362 (mpt) REVERT: D 162 LYS cc_start: 0.8656 (pttt) cc_final: 0.8186 (tppt) REVERT: D 242 ASP cc_start: 0.8389 (m-30) cc_final: 0.7833 (t0) REVERT: D 305 MET cc_start: 0.8634 (mpp) cc_final: 0.8238 (mpt) outliers start: 14 outliers final: 7 residues processed: 84 average time/residue: 1.3200 time to fit residues: 122.8452 Evaluate side-chains 79 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 128 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15150 Z= 0.181 Angle : 0.548 11.620 20654 Z= 0.262 Chirality : 0.039 0.163 2250 Planarity : 0.004 0.033 2648 Dihedral : 7.394 74.550 2088 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.71 % Allowed : 12.86 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.09 (0.20), residues: 1830 helix: 2.59 (0.20), residues: 686 sheet: 0.85 (0.28), residues: 348 loop : -1.09 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 24 HIS 0.005 0.001 HIS C 206 PHE 0.013 0.001 PHE B 510 TYR 0.011 0.001 TYR D 250 ARG 0.009 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8134 (mt0) cc_final: 0.7374 (mm-40) REVERT: B 414 GLN cc_start: 0.8139 (mt0) cc_final: 0.7371 (mm-40) REVERT: C 90 ASP cc_start: 0.8074 (m-30) cc_final: 0.7759 (m-30) REVERT: C 162 LYS cc_start: 0.8687 (pttt) cc_final: 0.8170 (tppt) REVERT: C 242 ASP cc_start: 0.8409 (m-30) cc_final: 0.7833 (t0) REVERT: C 305 MET cc_start: 0.8650 (mpp) cc_final: 0.8259 (mpt) REVERT: D 90 ASP cc_start: 0.8091 (m-30) cc_final: 0.7789 (m-30) REVERT: D 162 LYS cc_start: 0.8648 (pttt) cc_final: 0.8175 (tppt) REVERT: D 242 ASP cc_start: 0.8381 (m-30) cc_final: 0.7814 (t0) REVERT: D 305 MET cc_start: 0.8628 (mpp) cc_final: 0.8236 (mpt) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 1.3829 time to fit residues: 131.4694 Evaluate side-chains 82 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.0070 chunk 172 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 181 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15150 Z= 0.172 Angle : 0.541 7.595 20654 Z= 0.259 Chirality : 0.039 0.162 2250 Planarity : 0.004 0.035 2648 Dihedral : 7.333 76.764 2088 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.71 % Allowed : 13.18 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.12 (0.20), residues: 1830 helix: 2.63 (0.20), residues: 686 sheet: 0.87 (0.28), residues: 348 loop : -1.08 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.005 0.001 HIS D 206 PHE 0.013 0.001 PHE B 510 TYR 0.011 0.001 TYR C 250 ARG 0.009 0.000 ARG C 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8158 (mt0) cc_final: 0.7409 (mm-40) REVERT: B 414 GLN cc_start: 0.8163 (mt0) cc_final: 0.7404 (mm-40) REVERT: C 90 ASP cc_start: 0.8066 (m-30) cc_final: 0.7756 (m-30) REVERT: C 162 LYS cc_start: 0.8682 (pttt) cc_final: 0.8173 (tppt) REVERT: C 242 ASP cc_start: 0.8414 (m-30) cc_final: 0.7842 (t0) REVERT: C 305 MET cc_start: 0.8616 (mpp) cc_final: 0.8240 (mpt) REVERT: D 90 ASP cc_start: 0.8068 (m-30) cc_final: 0.7724 (m-30) REVERT: D 162 LYS cc_start: 0.8690 (pttt) cc_final: 0.8187 (tppt) REVERT: D 242 ASP cc_start: 0.8380 (m-30) cc_final: 0.7811 (t0) REVERT: D 305 MET cc_start: 0.8614 (mpp) cc_final: 0.8233 (mpt) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 1.3802 time to fit residues: 131.6331 Evaluate side-chains 79 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 24 TRP Chi-restraints excluded: chain D residue 24 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066084 restraints weight = 29942.232| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.05 r_work: 0.2905 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15150 Z= 0.187 Angle : 0.548 7.419 20654 Z= 0.262 Chirality : 0.039 0.163 2250 Planarity : 0.004 0.036 2648 Dihedral : 7.349 77.722 2088 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.58 % Allowed : 13.37 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1830 helix: 2.59 (0.20), residues: 686 sheet: 0.86 (0.28), residues: 348 loop : -1.06 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 24 HIS 0.005 0.001 HIS C 206 PHE 0.013 0.001 PHE A 510 TYR 0.012 0.001 TYR D 250 ARG 0.009 0.000 ARG C 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4474.48 seconds wall clock time: 79 minutes 32.11 seconds (4772.11 seconds total)