Starting phenix.real_space_refine on Fri May 23 18:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ep0_28494/05_2025/8ep0_28494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ep0_28494/05_2025/8ep0_28494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ep0_28494/05_2025/8ep0_28494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ep0_28494/05_2025/8ep0_28494.map" model { file = "/net/cci-nas-00/data/ceres_data/8ep0_28494/05_2025/8ep0_28494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ep0_28494/05_2025/8ep0_28494.cif" } resolution = 4.9 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= 0.004 sd= 0.019 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 116 5.16 5 C 15696 2.51 5 N 4108 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Restraints were copied for chains: G, F, H, C, B, D Time building chain proxies: 12.87, per 1000 atoms: 0.53 Number of scatterers: 24408 At special positions: 0 Unit cell: (169.56, 169.56, 149.04, 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 116 16.00 O 4488 8.00 N 4108 7.00 C 15696 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=0, symmetry=0 Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.5 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 65.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 Processing helix chain 'A' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.059A pdb=" N ASP B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 242 Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'B' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 4.114A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR B 347 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 545 through 552 Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 647 through 657 Processing helix chain 'B' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 707 through 722 Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.057A pdb=" N ASP C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 269 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N MET C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 4.094A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR C 347 " --> pdb=" O HIS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 473 removed outlier: 3.918A pdb=" N THR C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.876A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.996A pdb=" N ASN D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.846A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 242 Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 248 through 269 Processing helix chain 'D' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 removed outlier: 4.566A pdb=" N TYR D 347 " --> pdb=" O HIS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 379 removed outlier: 3.649A pdb=" N LEU D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 390 through 400 Processing helix chain 'D' and resid 418 through 435 Processing helix chain 'D' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 521 Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 545 through 552 Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 647 through 657 Processing helix chain 'D' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'D' and resid 707 through 722 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'H' and resid 6 through 10 Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE A 42 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 34 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 93 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY A 275 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS A 592 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL A 634 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN A 603 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE B 42 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN B 34 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 125 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 93 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY B 275 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS B 592 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B 672 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL B 634 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 609 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 603 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 587 through 588 removed outlier: 4.356A pdb=" N ALA B 628 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.590A pdb=" N ILE C 42 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN C 34 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 93 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 275 removed outlier: 4.898A pdb=" N GLY C 275 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS C 592 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL C 634 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN C 603 " --> pdb=" O VAL C 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE D 42 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN D 34 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 125 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 93 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY D 275 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS D 592 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 672 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL D 634 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 609 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN D 603 " --> pdb=" O VAL D 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA D 628 " --> pdb=" O VAL D 588 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4536 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: 8.50 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7950 1.34 - 1.46: 4433 1.46 - 1.58: 12409 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 24964 Sorted by residual: bond pdb=" N PHE C 359 " pdb=" CA PHE C 359 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.17e-02 7.31e+03 4.25e+00 bond pdb=" N PHE B 359 " pdb=" CA PHE B 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.99e+00 bond pdb=" N PHE A 359 " pdb=" CA PHE A 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.97e+00 bond pdb=" N PHE D 359 " pdb=" CA PHE D 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.70e+00 bond pdb=" CD1 TYR B 428 " pdb=" CE1 TYR B 428 " ideal model delta sigma weight residual 1.382 1.324 0.058 3.00e-02 1.11e+03 3.70e+00 ... (remaining 24959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 32930 1.89 - 3.79: 1034 3.79 - 5.68: 164 5.68 - 7.57: 28 7.57 - 9.47: 8 Bond angle restraints: 34164 Sorted by residual: angle pdb=" N MET B 431 " pdb=" CA MET B 431 " pdb=" CB MET B 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.70e+01 angle pdb=" N MET D 431 " pdb=" CA MET D 431 " pdb=" CB MET D 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.69e+01 angle pdb=" N MET C 431 " pdb=" CA MET C 431 " pdb=" CB MET C 431 " ideal model delta sigma weight residual 110.01 102.52 7.49 1.45e+00 4.76e-01 2.67e+01 angle pdb=" N MET A 431 " pdb=" CA MET A 431 " pdb=" CB MET A 431 " ideal model delta sigma weight residual 110.01 102.53 7.48 1.45e+00 4.76e-01 2.66e+01 angle pdb=" C LYS B 450 " pdb=" CA LYS B 450 " pdb=" CB LYS B 450 " ideal model delta sigma weight residual 109.67 118.57 -8.90 2.01e+00 2.48e-01 1.96e+01 ... (remaining 34159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 13283 15.64 - 31.29: 966 31.29 - 46.93: 171 46.93 - 62.57: 32 62.57 - 78.21: 28 Dihedral angle restraints: 14480 sinusoidal: 4608 harmonic: 9872 Sorted by residual: dihedral pdb=" CA TYR D 499 " pdb=" C TYR D 499 " pdb=" N GLN D 500 " pdb=" CA GLN D 500 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR A 499 " pdb=" C TYR A 499 " pdb=" N GLN A 500 " pdb=" CA GLN A 500 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR C 499 " pdb=" C TYR C 499 " pdb=" N GLN C 500 " pdb=" CA GLN C 500 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3612 0.078 - 0.156: 348 0.156 - 0.234: 28 0.234 - 0.312: 10 0.312 - 0.389: 10 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CB ILE C 378 " pdb=" CA ILE C 378 " pdb=" CG1 ILE C 378 " pdb=" CG2 ILE C 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE D 378 " pdb=" CA ILE D 378 " pdb=" CG1 ILE D 378 " pdb=" CG2 ILE D 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 4005 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 47 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" CG ASP C 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP C 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 47 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" CG ASP D 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP D 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP D 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 47 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" CG ASP A 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP A 47 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP A 47 " -0.023 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4831 2.77 - 3.30: 27126 3.30 - 3.83: 41904 3.83 - 4.37: 46091 4.37 - 4.90: 75741 Nonbonded interactions: 195693 Sorted by model distance: nonbonded pdb=" OG SER B 418 " pdb=" OD1 ASN B 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 418 " pdb=" OD1 ASN A 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 418 " pdb=" OD1 ASN C 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER D 418 " pdb=" OD1 ASN D 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 2.239 3.040 ... (remaining 195688 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: 0.18 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 1.380 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: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 53.590 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.004 0.071 24964 Z= 0.196 Angle : 0.785 9.468 34164 Z= 0.454 Chirality : 0.051 0.389 4008 Planarity : 0.006 0.103 4416 Dihedral : 12.186 78.213 8080 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3340 helix: 0.25 (0.12), residues: 1928 sheet: 0.88 (0.36), residues: 172 loop : -0.21 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 108 HIS 0.010 0.001 HIS D 364 PHE 0.058 0.004 PHE B 17 TYR 0.040 0.003 TYR D 428 ARG 0.023 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.10439 ( 1572) hydrogen bonds : angle 5.44805 ( 4536) covalent geometry : bond 0.00395 (24964) covalent geometry : angle 0.78531 (34164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.158 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.2037 time to fit residues: 2.5916 Evaluate side-chains 9 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.191 Evaluate side-chains 83 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9375 (tpp) cc_final: 0.9172 (tpp) REVERT: A 224 ILE cc_start: 0.9522 (pt) cc_final: 0.9231 (mm) REVERT: A 423 TYR cc_start: 0.8796 (t80) cc_final: 0.8410 (t80) REVERT: A 427 LEU cc_start: 0.9212 (tp) cc_final: 0.8876 (mt) REVERT: A 568 MET cc_start: 0.9272 (mmp) cc_final: 0.8953 (mmp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1422 time to fit residues: 16.9547 Evaluate side-chains 64 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.0870 chunk 254 optimal weight: 8.9990 chunk 141 optimal weight: 0.0030 chunk 86 optimal weight: 0.0050 chunk 171 optimal weight: 20.0000 chunk 136 optimal weight: 0.0040 chunk 263 optimal weight: 0.0170 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 196 optimal weight: 30.0000 chunk 305 optimal weight: 30.0000 overall best weight: 0.0232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.038165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027676 restraints weight = 15107.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027676 restraints weight = 15911.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027676 restraints weight = 15911.086| |-----------------------------------------------------------------------------| r_work (final): 0.2757 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.044743 restraints weight = 57370.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045797 restraints weight = 38218.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046563 restraints weight = 27847.917| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24964 Z= 0.133 Angle : 0.602 7.833 34164 Z= 0.326 Chirality : 0.042 0.170 4008 Planarity : 0.004 0.051 4416 Dihedral : 5.064 60.718 3584 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3340 helix: 0.71 (0.12), residues: 1960 sheet: 0.94 (0.37), residues: 172 loop : -0.14 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 250 HIS 0.005 0.001 HIS A 486 PHE 0.019 0.002 PHE B 452 TYR 0.020 0.001 TYR D 428 ARG 0.011 0.001 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1572) hydrogen bonds : angle 4.76133 ( 4536) covalent geometry : bond 0.00254 (24964) covalent geometry : angle 0.60171 (34164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.109 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0521 time to fit residues: 0.8140 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.109 Evaluate side-chains 85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9603 (t80) cc_final: 0.9349 (t80) REVERT: B 365 TRP cc_start: 0.9444 (m100) cc_final: 0.9169 (m100) REVERT: B 377 GLU cc_start: 0.9503 (tp30) cc_final: 0.9140 (tp30) REVERT: B 449 GLU cc_start: 0.9512 (mt-10) cc_final: 0.9302 (mt-10) REVERT: B 536 MET cc_start: 0.9406 (mmp) cc_final: 0.9146 (mmm) REVERT: B 568 MET cc_start: 0.9500 (mmp) cc_final: 0.9188 (mmp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1703 time to fit residues: 19.4596 Evaluate side-chains 66 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 334 optimal weight: 0.0170 chunk 89 optimal weight: 0.0770 chunk 218 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 236 optimal weight: 20.0000 chunk 77 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 chunk 60 optimal weight: 0.0040 chunk 12 optimal weight: 20.0000 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.037507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027462 restraints weight = 14707.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027462 restraints weight = 15288.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027462 restraints weight = 15288.076| |-----------------------------------------------------------------------------| r_work (final): 0.2744 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.056046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044472 restraints weight = 59178.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045483 restraints weight = 38745.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046224 restraints weight = 28318.818| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24964 Z= 0.140 Angle : 0.624 8.656 34164 Z= 0.337 Chirality : 0.045 0.337 4008 Planarity : 0.006 0.098 4416 Dihedral : 5.035 59.958 3584 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.18 % Allowed : 3.42 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1956 sheet: 1.24 (0.40), residues: 156 loop : -0.20 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 108 HIS 0.008 0.001 HIS D 364 PHE 0.048 0.003 PHE C 49 TYR 0.047 0.002 TYR B 100 ARG 0.021 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1572) hydrogen bonds : angle 4.67790 ( 4536) covalent geometry : bond 0.00286 (24964) covalent geometry : angle 0.62408 (34164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0524 time to fit residues: 0.7994 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.102 Evaluate side-chains 81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9460 (t80) cc_final: 0.9245 (t80) REVERT: B 359 PHE cc_start: 0.9592 (t80) cc_final: 0.9390 (t80) REVERT: B 365 TRP cc_start: 0.9391 (m100) cc_final: 0.9071 (m100) REVERT: B 366 MET cc_start: 0.9139 (mmp) cc_final: 0.8563 (ptp) REVERT: B 377 GLU cc_start: 0.9527 (tp30) cc_final: 0.9161 (tp30) REVERT: B 424 ILE cc_start: 0.9255 (pt) cc_final: 0.8786 (pt) REVERT: B 536 MET cc_start: 0.9472 (mmp) cc_final: 0.8940 (mmt) REVERT: B 539 ASP cc_start: 0.9352 (t70) cc_final: 0.9020 (m-30) REVERT: B 568 MET cc_start: 0.9506 (mmp) cc_final: 0.9212 (mmp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1371 time to fit residues: 15.1276 Evaluate side-chains 63 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 63 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 283 optimal weight: 6.9990 chunk 132 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 243 optimal weight: 0.0970 chunk 79 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 279 optimal weight: 30.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.027093 restraints weight = 15321.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027078 restraints weight = 14281.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027078 restraints weight = 14949.151| |-----------------------------------------------------------------------------| r_work (final): 0.2727 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044458 restraints weight = 59774.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045521 restraints weight = 39419.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046269 restraints weight = 28557.520| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24964 Z= 0.141 Angle : 0.622 8.645 34164 Z= 0.336 Chirality : 0.045 0.337 4008 Planarity : 0.006 0.097 4416 Dihedral : 5.034 59.957 3584 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1956 sheet: 1.24 (0.40), residues: 156 loop : -0.21 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 108 HIS 0.008 0.001 HIS C 364 PHE 0.047 0.003 PHE C 49 TYR 0.047 0.002 TYR D 100 ARG 0.022 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 1572) hydrogen bonds : angle 4.67850 ( 4536) covalent geometry : bond 0.00292 (24964) covalent geometry : angle 0.62240 (34164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0586 time to fit residues: 0.9136 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.100 Evaluate side-chains 76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9487 (t80) cc_final: 0.9249 (t80) REVERT: B 359 PHE cc_start: 0.9583 (t80) cc_final: 0.9379 (t80) REVERT: B 365 TRP cc_start: 0.9387 (m100) cc_final: 0.9071 (m100) REVERT: B 366 MET cc_start: 0.9076 (mmp) cc_final: 0.8569 (ptp) REVERT: B 377 GLU cc_start: 0.9538 (tp30) cc_final: 0.9148 (tp30) REVERT: B 424 ILE cc_start: 0.9444 (pt) cc_final: 0.8797 (pt) REVERT: B 449 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9228 (mt-10) REVERT: B 478 MET cc_start: 0.9198 (tpt) cc_final: 0.8791 (tpt) REVERT: B 536 MET cc_start: 0.9471 (mmp) cc_final: 0.8954 (mmt) REVERT: B 539 ASP cc_start: 0.9358 (t70) cc_final: 0.9025 (m-30) REVERT: B 568 MET cc_start: 0.9506 (mmp) cc_final: 0.9212 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1579 time to fit residues: 16.5826 Evaluate side-chains 63 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 12 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 229 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 237 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 258 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 0.7980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.037590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.027376 restraints weight = 14970.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.027371 restraints weight = 14999.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.027359 restraints weight = 15104.494| |-----------------------------------------------------------------------------| r_work (final): 0.2738 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044589 restraints weight = 58415.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045627 restraints weight = 38279.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046381 restraints weight = 27867.103| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24964 Z= 0.130 Angle : 0.602 7.062 34164 Z= 0.325 Chirality : 0.045 0.411 4008 Planarity : 0.005 0.080 4416 Dihedral : 4.948 59.056 3584 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % 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: 0.31 (0.15), residues: 3340 helix: 0.52 (0.12), residues: 1956 sheet: 1.11 (0.40), residues: 156 loop : -0.24 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 108 HIS 0.007 0.001 HIS A 364 PHE 0.049 0.003 PHE D 17 TYR 0.048 0.003 TYR D 100 ARG 0.021 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 1572) hydrogen bonds : angle 4.59665 ( 4536) covalent geometry : bond 0.00270 (24964) covalent geometry : angle 0.60242 (34164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.105 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0540 time to fit residues: 0.8399 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.103 Evaluate side-chains 76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9451 (t80) cc_final: 0.9217 (t80) REVERT: B 359 PHE cc_start: 0.9586 (t80) cc_final: 0.9374 (t80) REVERT: B 365 TRP cc_start: 0.9368 (m100) cc_final: 0.9029 (m100) REVERT: B 366 MET cc_start: 0.9152 (mmp) cc_final: 0.8681 (ptp) REVERT: B 377 GLU cc_start: 0.9503 (tp30) cc_final: 0.9102 (tp30) REVERT: B 435 THR cc_start: 0.9077 (p) cc_final: 0.8865 (p) REVERT: B 449 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9082 (mt-10) REVERT: B 536 MET cc_start: 0.9400 (mmp) cc_final: 0.9165 (mmm) REVERT: B 539 ASP cc_start: 0.9283 (t70) cc_final: 0.9021 (m-30) REVERT: B 568 MET cc_start: 0.9498 (mmp) cc_final: 0.9191 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1396 time to fit residues: 14.8208 Evaluate side-chains 64 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 131 optimal weight: 0.0060 chunk 315 optimal weight: 40.0000 chunk 323 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 50.0000 chunk 153 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 209 optimal weight: 40.0000 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.037577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027484 restraints weight = 15336.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.027251 restraints weight = 15707.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.027251 restraints weight = 15260.439| |-----------------------------------------------------------------------------| r_work (final): 0.2731 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044484 restraints weight = 57793.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045518 restraints weight = 38271.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046237 restraints weight = 27967.060| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24964 Z= 0.118 Angle : 0.590 7.091 34164 Z= 0.316 Chirality : 0.045 0.438 4008 Planarity : 0.005 0.079 4416 Dihedral : 4.794 57.045 3584 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1948 sheet: 1.09 (0.38), residues: 180 loop : -0.26 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 108 HIS 0.005 0.001 HIS D 364 PHE 0.052 0.003 PHE B 17 TYR 0.047 0.003 TYR D 100 ARG 0.020 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1572) hydrogen bonds : angle 4.52633 ( 4536) covalent geometry : bond 0.00233 (24964) covalent geometry : angle 0.58976 (34164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.101 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0519 time to fit residues: 0.8160 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.106 Evaluate side-chains 81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9577 (t80) cc_final: 0.9302 (t80) REVERT: B 365 TRP cc_start: 0.9334 (m100) cc_final: 0.9016 (m100) REVERT: B 366 MET cc_start: 0.9254 (mmp) cc_final: 0.8873 (ptp) REVERT: B 377 GLU cc_start: 0.9512 (tp30) cc_final: 0.9127 (tp30) REVERT: B 449 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9071 (mt-10) REVERT: B 536 MET cc_start: 0.9403 (mmp) cc_final: 0.9124 (mmm) REVERT: B 539 ASP cc_start: 0.9319 (t70) cc_final: 0.9000 (m-30) REVERT: B 568 MET cc_start: 0.9476 (mmp) cc_final: 0.9174 (mmp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1455 time to fit residues: 16.1334 Evaluate side-chains 62 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 172 optimal weight: 9.9990 chunk 89 optimal weight: 0.0000 chunk 327 optimal weight: 30.0000 chunk 59 optimal weight: 0.9980 chunk 322 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 157 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 208 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.037425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.027604 restraints weight = 15651.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.027621 restraints weight = 16607.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.027770 restraints weight = 14860.242| |-----------------------------------------------------------------------------| r_work (final): 0.2758 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042903 restraints weight = 51899.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043893 restraints weight = 35309.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044633 restraints weight = 26422.417| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24964 Z= 0.130 Angle : 0.612 6.935 34164 Z= 0.325 Chirality : 0.045 0.443 4008 Planarity : 0.005 0.075 4416 Dihedral : 4.775 56.651 3584 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1952 sheet: 1.10 (0.39), residues: 180 loop : -0.31 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 108 HIS 0.006 0.001 HIS A 364 PHE 0.097 0.003 PHE A 17 TYR 0.047 0.003 TYR C 100 ARG 0.018 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1572) hydrogen bonds : angle 4.51633 ( 4536) covalent geometry : bond 0.00279 (24964) covalent geometry : angle 0.61157 (34164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.102 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0506 time to fit residues: 0.7935 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.095 Evaluate side-chains 78 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9520 (t80) cc_final: 0.9115 (t80) REVERT: B 359 PHE cc_start: 0.9580 (t80) cc_final: 0.9300 (t80) REVERT: B 365 TRP cc_start: 0.9368 (m100) cc_final: 0.9080 (m100) REVERT: B 366 MET cc_start: 0.9262 (mmp) cc_final: 0.8893 (ptp) REVERT: B 377 GLU cc_start: 0.9585 (tp30) cc_final: 0.9192 (tp30) REVERT: B 449 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9170 (mt-10) REVERT: B 478 MET cc_start: 0.9186 (tpt) cc_final: 0.8814 (tpt) REVERT: B 568 MET cc_start: 0.9518 (mmp) cc_final: 0.9229 (mmp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1326 time to fit residues: 14.4376 Evaluate side-chains 60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 0.0010 chunk 107 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 73 optimal weight: 100.0000 chunk 216 optimal weight: 0.4980 chunk 319 optimal weight: 40.0000 chunk 278 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 overall best weight: 2.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.027620 restraints weight = 15578.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.027552 restraints weight = 15711.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.027595 restraints weight = 15443.026| |-----------------------------------------------------------------------------| r_work (final): 0.2756 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.056014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044538 restraints weight = 58147.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045538 restraints weight = 38863.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046268 restraints weight = 28698.487| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24964 Z= 0.130 Angle : 0.612 6.935 34164 Z= 0.325 Chirality : 0.045 0.443 4008 Planarity : 0.005 0.075 4416 Dihedral : 4.775 56.651 3584 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1952 sheet: 1.10 (0.39), residues: 180 loop : -0.31 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 108 HIS 0.006 0.001 HIS C 364 PHE 0.097 0.003 PHE A 17 TYR 0.047 0.003 TYR D 100 ARG 0.018 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1572) hydrogen bonds : angle 4.51633 ( 4536) covalent geometry : bond 0.00279 (24964) covalent geometry : angle 0.61157 (34164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.115 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0569 time to fit residues: 0.8855 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.107 Evaluate side-chains 77 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9589 (t80) cc_final: 0.9173 (t80) REVERT: B 359 PHE cc_start: 0.9562 (t80) cc_final: 0.9280 (t80) REVERT: B 365 TRP cc_start: 0.9386 (m100) cc_final: 0.9114 (m100) REVERT: B 366 MET cc_start: 0.9220 (mmp) cc_final: 0.8754 (ptp) REVERT: B 377 GLU cc_start: 0.9567 (tp30) cc_final: 0.9176 (tp30) REVERT: B 449 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9164 (mt-10) REVERT: B 478 MET cc_start: 0.9200 (tpt) cc_final: 0.8826 (tpt) REVERT: B 568 MET cc_start: 0.9512 (mmp) cc_final: 0.9219 (mmp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1402 time to fit residues: 15.1563 Evaluate side-chains 59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 32 optimal weight: 1.9990 chunk 169 optimal weight: 30.0000 chunk 296 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 159 optimal weight: 0.0040 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 285 optimal weight: 0.0050 chunk 164 optimal weight: 0.6980 chunk 306 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.027596 restraints weight = 15618.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.027564 restraints weight = 15747.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.027597 restraints weight = 15111.096| |-----------------------------------------------------------------------------| r_work (final): 0.2755 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.044434 restraints weight = 58306.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045449 restraints weight = 39082.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046175 restraints weight = 28678.803| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24964 Z= 0.130 Angle : 0.612 6.935 34164 Z= 0.325 Chirality : 0.045 0.443 4008 Planarity : 0.005 0.075 4416 Dihedral : 4.775 56.651 3584 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1952 sheet: 1.10 (0.39), residues: 180 loop : -0.31 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 108 HIS 0.006 0.001 HIS B 364 PHE 0.097 0.003 PHE A 17 TYR 0.047 0.003 TYR B 100 ARG 0.018 0.001 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1572) hydrogen bonds : angle 4.51633 ( 4536) covalent geometry : bond 0.00279 (24964) covalent geometry : angle 0.61157 (34164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.146 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0602 time to fit residues: 0.9563 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.162 Evaluate side-chains 76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9571 (t80) cc_final: 0.9159 (t80) REVERT: B 359 PHE cc_start: 0.9569 (t80) cc_final: 0.9288 (t80) REVERT: B 365 TRP cc_start: 0.9367 (m100) cc_final: 0.9079 (m100) REVERT: B 366 MET cc_start: 0.9229 (mmp) cc_final: 0.8759 (ptp) REVERT: B 377 GLU cc_start: 0.9566 (tp30) cc_final: 0.9160 (tp30) REVERT: B 449 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9146 (mt-10) REVERT: B 478 MET cc_start: 0.9193 (tpt) cc_final: 0.8818 (tpt) REVERT: B 568 MET cc_start: 0.9513 (mmp) cc_final: 0.9220 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1521 time to fit residues: 16.5200 Evaluate side-chains 59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 199 optimal weight: 10.0000 chunk 240 optimal weight: 0.0000 chunk 317 optimal weight: 0.0970 chunk 6 optimal weight: 4.9990 chunk 269 optimal weight: 0.1980 chunk 160 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 168 optimal weight: 0.0060 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027636 restraints weight = 15678.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.027504 restraints weight = 16082.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.027447 restraints weight = 16220.334| |-----------------------------------------------------------------------------| r_work (final): 0.2752 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.044421 restraints weight = 58636.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045443 restraints weight = 39232.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046167 restraints weight = 28757.822| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24964 Z= 0.130 Angle : 0.612 6.935 34164 Z= 0.325 Chirality : 0.045 0.443 4008 Planarity : 0.005 0.075 4416 Dihedral : 4.775 56.651 3584 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1952 sheet: 1.10 (0.39), residues: 180 loop : -0.31 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 108 HIS 0.006 0.001 HIS B 364 PHE 0.097 0.003 PHE C 17 TYR 0.047 0.003 TYR C 100 ARG 0.018 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1572) hydrogen bonds : angle 4.51633 ( 4536) covalent geometry : bond 0.00279 (24964) covalent geometry : angle 0.61157 (34164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.101 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0525 time to fit residues: 0.8072 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.106 Evaluate side-chains 76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9571 (t80) cc_final: 0.9159 (t80) REVERT: B 359 PHE cc_start: 0.9569 (t80) cc_final: 0.9288 (t80) REVERT: B 365 TRP cc_start: 0.9366 (m100) cc_final: 0.9079 (m100) REVERT: B 366 MET cc_start: 0.9230 (mmp) cc_final: 0.8760 (ptp) REVERT: B 377 GLU cc_start: 0.9566 (tp30) cc_final: 0.9160 (tp30) REVERT: B 449 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9148 (mt-10) REVERT: B 478 MET cc_start: 0.9194 (tpt) cc_final: 0.8819 (tpt) REVERT: B 568 MET cc_start: 0.9513 (mmp) cc_final: 0.9220 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1314 time to fit residues: 13.9639 Evaluate side-chains 59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 192 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 113 optimal weight: 0.0000 chunk 98 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 chunk 186 optimal weight: 0.0040 chunk 17 optimal weight: 50.0000 chunk 134 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.037425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.027518 restraints weight = 15929.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.027556 restraints weight = 16021.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.027556 restraints weight = 14673.298| |-----------------------------------------------------------------------------| r_work (final): 0.2755 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044386 restraints weight = 59455.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045410 restraints weight = 39666.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046145 restraints weight = 29047.349| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24964 Z= 0.130 Angle : 0.612 6.935 34164 Z= 0.325 Chirality : 0.045 0.443 4008 Planarity : 0.005 0.075 4416 Dihedral : 4.775 56.651 3584 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3340 helix: 0.57 (0.12), residues: 1952 sheet: 1.10 (0.39), residues: 180 loop : -0.31 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 108 HIS 0.006 0.001 HIS B 364 PHE 0.097 0.003 PHE C 17 TYR 0.047 0.003 TYR D 100 ARG 0.018 0.001 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1572) hydrogen bonds : angle 4.51633 ( 4536) covalent geometry : bond 0.00279 (24964) covalent geometry : angle 0.61157 (34164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.43 seconds wall clock time: 78 minutes 23.80 seconds (4703.80 seconds total)