Starting phenix.real_space_refine on Sat Sep 12 22:13:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uw9_20920/09_2026/6uw9_20920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uw9_20920/09_2026/6uw9_20920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uw9_20920/09_2026/6uw9_20920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uw9_20920/09_2026/6uw9_20920.map" model { file = "/net/cci-nas-00/data/ceres_data/6uw9_20920/09_2026/6uw9_20920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uw9_20920/09_2026/6uw9_20920.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12340 2.51 5 N 3136 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18924 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4731 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 571} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Restraints were copied for chains: B, C, D Time building chain proxies: 4.63, per 1000 atoms: 0.24 Number of scatterers: 18924 At special positions: 0 Unit cell: (159.5, 159.5, 117.7, 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 112 16.00 O 3336 8.00 N 3136 7.00 C 12340 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: 1.58 Conformation dependent library (CDL) restraints added in 846.9 milliseconds 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 67.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 4.008A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.621A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 569 through 586 removed outlier: 4.360A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.883A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 706 removed outlier: 3.605A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.438A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.537A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 335 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 removed outlier: 4.008A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.904A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.883A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.166A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.622A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 567' Processing helix chain 'B' and resid 569 through 586 removed outlier: 4.361A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 706 removed outlier: 3.606A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.611A pdb=" N LEU C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.591A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.934A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C 335 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 4.007A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 501 removed outlier: 4.236A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.622A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 563 through 567' Processing helix chain 'C' and resid 569 through 586 removed outlier: 4.361A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 679 removed outlier: 3.704A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 706 removed outlier: 3.606A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.610A pdb=" N LEU D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 4.437A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.671A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.592A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.538A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.912A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.935A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 335 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 removed outlier: 4.007A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.903A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.884A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 431 " --> pdb=" O THR D 427 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 462 removed outlier: 3.526A pdb=" N ARG D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 501 removed outlier: 4.235A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.165A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.826A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.164A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.621A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 563 through 567' Processing helix chain 'D' and resid 569 through 586 removed outlier: 4.360A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.884A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 679 removed outlier: 3.703A pdb=" N PHE D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 706 removed outlier: 3.605A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.824A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.945A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2940 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: 3.17 Time building geometry restraints manager: 2.16 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: 5464 1.34 - 1.46: 3429 1.46 - 1.57: 10235 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 19320 Sorted by residual: bond pdb=" C PRO B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.71e+01 bond pdb=" C PRO D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.70e+01 bond pdb=" C PRO C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.332 1.219 0.113 1.29e-02 6.01e+03 7.70e+01 bond pdb=" C PRO A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.332 1.220 0.112 1.29e-02 6.01e+03 7.59e+01 bond pdb=" C GLU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.331 1.386 -0.054 7.90e-03 1.60e+04 4.75e+01 ... (remaining 19315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 25675 3.29 - 6.59: 341 6.59 - 9.88: 64 9.88 - 13.17: 24 13.17 - 16.47: 16 Bond angle restraints: 26120 Sorted by residual: angle pdb=" CA PRO A 424 " pdb=" C PRO A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 118.81 103.11 15.70 1.61e+00 3.86e-01 9.51e+01 angle pdb=" CA PRO C 424 " pdb=" C PRO C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 118.81 103.15 15.66 1.61e+00 3.86e-01 9.46e+01 angle pdb=" CA PRO B 424 " pdb=" C PRO B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 118.81 103.17 15.64 1.61e+00 3.86e-01 9.44e+01 angle pdb=" CA PRO D 424 " pdb=" C PRO D 424 " pdb=" N LEU D 425 " ideal model delta sigma weight residual 118.81 103.17 15.64 1.61e+00 3.86e-01 9.44e+01 angle pdb=" C PRO A 424 " pdb=" N LEU A 425 " pdb=" CA LEU A 425 " ideal model delta sigma weight residual 122.60 106.13 16.47 1.88e+00 2.83e-01 7.67e+01 ... (remaining 26115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 9869 16.86 - 33.72: 1254 33.72 - 50.59: 277 50.59 - 67.45: 28 67.45 - 84.31: 16 Dihedral angle restraints: 11444 sinusoidal: 4600 harmonic: 6844 Sorted by residual: dihedral pdb=" CA ILE A 199 " pdb=" C ILE A 199 " pdb=" N LEU A 200 " pdb=" CA LEU A 200 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N LEU B 200 " pdb=" CA LEU B 200 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE C 199 " pdb=" C ILE C 199 " pdb=" N LEU C 200 " pdb=" CA LEU C 200 " ideal model delta harmonic sigma weight residual 180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2332 0.064 - 0.127: 528 0.127 - 0.191: 106 0.191 - 0.254: 26 0.254 - 0.318: 8 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA ASP B 586 " pdb=" N ASP B 586 " pdb=" C ASP B 586 " pdb=" CB ASP B 586 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA ASP A 586 " pdb=" N ASP A 586 " pdb=" C ASP A 586 " pdb=" CB ASP A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ASP C 586 " pdb=" N ASP C 586 " pdb=" C ASP C 586 " pdb=" CB ASP C 586 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2997 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 343 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 344 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 344 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO D 344 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.044 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 152 2.53 - 3.12: 12859 3.12 - 3.71: 29738 3.71 - 4.31: 37668 4.31 - 4.90: 62242 Nonbonded interactions: 142659 Sorted by model distance: nonbonded pdb=" SD MET A 431 " pdb=" NH1 ARG A 716 " model vdw 1.932 3.480 nonbonded pdb=" SD MET D 431 " pdb=" NH1 ARG D 716 " model vdw 1.933 3.480 nonbonded pdb=" SD MET C 431 " pdb=" NH1 ARG C 716 " model vdw 1.933 3.480 nonbonded pdb=" SD MET B 431 " pdb=" NH1 ARG B 716 " model vdw 1.933 3.480 nonbonded pdb=" SD MET D 431 " pdb=" CZ ARG D 716 " model vdw 1.973 3.630 ... (remaining 142654 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.820 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.005 0.113 19320 Z= 0.298 Angle : 1.144 16.467 26120 Z= 0.630 Chirality : 0.060 0.318 3000 Planarity : 0.007 0.081 3236 Dihedral : 15.426 84.310 6996 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.20 % Allowed : 11.22 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.13), residues: 2288 helix: -3.02 (0.09), residues: 1424 sheet: -1.63 (0.86), residues: 40 loop : -3.58 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.015 0.002 TYR B 451 PHE 0.034 0.002 PHE D 656 TRP 0.012 0.001 TRP D 380 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.30 (19320) covalent geometry : angle 1.14426 / 0.63 (26120) hydrogen bonds : bond 0.16155 / 11.07 ( 996) hydrogen bonds : angle 6.92352 / 4.85 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 532 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8780 (m-40) cc_final: 0.8363 (p0) REVERT: A 268 LEU cc_start: 0.9407 (tp) cc_final: 0.9162 (tp) REVERT: A 366 LYS cc_start: 0.8790 (mppt) cc_final: 0.8357 (mmmt) REVERT: A 562 MET cc_start: 0.8934 (tpp) cc_final: 0.8636 (tpp) REVERT: A 592 PHE cc_start: 0.8665 (t80) cc_final: 0.8415 (t80) REVERT: A 595 ILE cc_start: 0.9398 (mm) cc_final: 0.9090 (tp) REVERT: A 672 MET cc_start: 0.9048 (tmm) cc_final: 0.8755 (tmm) REVERT: B 188 ARG cc_start: 0.8723 (mmp-170) cc_final: 0.8385 (tpp-160) REVERT: B 205 ASN cc_start: 0.8811 (m-40) cc_final: 0.8362 (p0) REVERT: B 268 LEU cc_start: 0.9425 (tp) cc_final: 0.9183 (tp) REVERT: B 366 LYS cc_start: 0.8792 (mppt) cc_final: 0.8379 (mmmt) REVERT: B 409 TYR cc_start: 0.8276 (m-10) cc_final: 0.6978 (m-10) REVERT: B 562 MET cc_start: 0.9010 (tpp) cc_final: 0.8740 (tpp) REVERT: B 574 MET cc_start: 0.8848 (mtm) cc_final: 0.8621 (mtm) REVERT: B 592 PHE cc_start: 0.8664 (t80) cc_final: 0.8364 (t80) REVERT: B 595 ILE cc_start: 0.9393 (mm) cc_final: 0.9039 (tp) REVERT: B 672 MET cc_start: 0.9067 (tmm) cc_final: 0.8738 (tmm) REVERT: C 188 ARG cc_start: 0.8726 (mmp-170) cc_final: 0.8514 (mmp80) REVERT: C 205 ASN cc_start: 0.8768 (m-40) cc_final: 0.8246 (p0) REVERT: C 268 LEU cc_start: 0.9419 (tp) cc_final: 0.9179 (tp) REVERT: C 366 LYS cc_start: 0.8864 (mppt) cc_final: 0.8474 (mmmt) REVERT: C 497 ILE cc_start: 0.9093 (tp) cc_final: 0.8871 (tt) REVERT: C 562 MET cc_start: 0.8998 (tpp) cc_final: 0.8718 (tpp) REVERT: C 572 MET cc_start: 0.8447 (tpp) cc_final: 0.7832 (mmm) REVERT: C 574 MET cc_start: 0.8835 (mtm) cc_final: 0.8605 (mtm) REVERT: C 592 PHE cc_start: 0.8701 (t80) cc_final: 0.8453 (t80) REVERT: C 595 ILE cc_start: 0.9390 (mm) cc_final: 0.9020 (tp) REVERT: C 672 MET cc_start: 0.9061 (tmm) cc_final: 0.8741 (tmm) REVERT: D 188 ARG cc_start: 0.8720 (mmp-170) cc_final: 0.8496 (mmp80) REVERT: D 205 ASN cc_start: 0.8816 (m-40) cc_final: 0.8358 (p0) REVERT: D 268 LEU cc_start: 0.9422 (tp) cc_final: 0.9173 (tp) REVERT: D 366 LYS cc_start: 0.8846 (mppt) cc_final: 0.8416 (mmmt) REVERT: D 497 ILE cc_start: 0.9089 (tp) cc_final: 0.8883 (tt) REVERT: D 562 MET cc_start: 0.8992 (tpp) cc_final: 0.8683 (tpp) REVERT: D 574 MET cc_start: 0.8863 (mtm) cc_final: 0.8616 (mtm) REVERT: D 592 PHE cc_start: 0.8690 (t80) cc_final: 0.8438 (t80) REVERT: D 595 ILE cc_start: 0.9397 (mm) cc_final: 0.9066 (tp) REVERT: D 672 MET cc_start: 0.9079 (tmm) cc_final: 0.8743 (tmm) REVERT: D 677 MET cc_start: 0.8556 (ttm) cc_final: 0.7923 (ttm) outliers start: 4 outliers final: 4 residues processed: 536 average time/residue: 0.1327 time to fit residues: 110.2108 Evaluate side-chains 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 371 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 561 ASN A 580 GLN A 671 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 570 GLN B 580 GLN B 671 ASN ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 561 ASN C 570 GLN C 580 GLN C 671 ASN ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 570 GLN D 580 GLN D 671 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097983 restraints weight = 39586.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100314 restraints weight = 25346.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101969 restraints weight = 18290.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103104 restraints weight = 14350.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103995 restraints weight = 11996.832| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19320 Z= 0.126 Angle : 0.653 9.015 26120 Z= 0.331 Chirality : 0.041 0.183 3000 Planarity : 0.005 0.069 3236 Dihedral : 4.986 21.241 2524 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.39 % Allowed : 6.15 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.16), residues: 2288 helix: -0.86 (0.13), residues: 1468 sheet: -1.44 (0.82), residues: 40 loop : -3.31 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 716 TYR 0.013 0.001 TYR A 661 PHE 0.019 0.001 PHE B 656 TRP 0.006 0.001 TRP A 739 HIS 0.002 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (19320) covalent geometry : angle 0.65343 / 0.33 (26120) hydrogen bonds : bond 0.04287 / 2.88 ( 996) hydrogen bonds : angle 4.30634 / 3.03 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 504 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6389 (mpp) cc_final: 0.6013 (mpp) REVERT: A 246 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7531 (ttpp) REVERT: A 366 LYS cc_start: 0.8837 (mppt) cc_final: 0.8335 (mmmt) REVERT: A 431 MET cc_start: 0.8632 (ttm) cc_final: 0.8223 (ttm) REVERT: A 527 PHE cc_start: 0.8126 (t80) cc_final: 0.7887 (t80) REVERT: A 555 MET cc_start: 0.8145 (tpp) cc_final: 0.7838 (tpp) REVERT: A 561 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8735 (t0) REVERT: A 562 MET cc_start: 0.9049 (tpp) cc_final: 0.8795 (tpp) REVERT: A 595 ILE cc_start: 0.9343 (mm) cc_final: 0.9025 (tp) REVERT: A 677 MET cc_start: 0.8280 (ttt) cc_final: 0.7969 (tpp) REVERT: A 740 THR cc_start: 0.7527 (m) cc_final: 0.7271 (p) REVERT: B 159 MET cc_start: 0.6544 (mpp) cc_final: 0.6091 (mpp) REVERT: B 205 ASN cc_start: 0.8600 (m-40) cc_final: 0.8382 (p0) REVERT: B 246 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7392 (ttpp) REVERT: B 366 LYS cc_start: 0.8826 (mppt) cc_final: 0.8390 (mmmt) REVERT: B 402 SER cc_start: 0.9078 (t) cc_final: 0.8843 (p) REVERT: B 431 MET cc_start: 0.8651 (ttm) cc_final: 0.8217 (ttm) REVERT: B 527 PHE cc_start: 0.8229 (t80) cc_final: 0.7974 (t80) REVERT: B 561 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8747 (t0) REVERT: B 562 MET cc_start: 0.9089 (tpp) cc_final: 0.8819 (tpp) REVERT: B 595 ILE cc_start: 0.9348 (mm) cc_final: 0.9007 (tp) REVERT: B 740 THR cc_start: 0.7446 (m) cc_final: 0.7153 (t) REVERT: C 159 MET cc_start: 0.6412 (mpp) cc_final: 0.6036 (mpp) REVERT: C 205 ASN cc_start: 0.8613 (m-40) cc_final: 0.8360 (p0) REVERT: C 246 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7442 (ttpp) REVERT: C 279 GLN cc_start: 0.7297 (tp40) cc_final: 0.6920 (tp-100) REVERT: C 283 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6696 (mt-10) REVERT: C 366 LYS cc_start: 0.8842 (mppt) cc_final: 0.8458 (mmmt) REVERT: C 402 SER cc_start: 0.9062 (t) cc_final: 0.8851 (p) REVERT: C 431 MET cc_start: 0.8707 (ttm) cc_final: 0.8308 (ttm) REVERT: C 497 ILE cc_start: 0.9062 (tp) cc_final: 0.8765 (tt) REVERT: C 561 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8725 (t0) REVERT: C 562 MET cc_start: 0.9102 (tpp) cc_final: 0.8796 (tpp) REVERT: C 595 ILE cc_start: 0.9346 (mm) cc_final: 0.9002 (tp) REVERT: C 743 LYS cc_start: 0.7865 (mttt) cc_final: 0.7628 (mmtt) REVERT: D 159 MET cc_start: 0.6532 (mpp) cc_final: 0.6076 (mpp) REVERT: D 205 ASN cc_start: 0.8589 (m-40) cc_final: 0.8376 (p0) REVERT: D 246 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7430 (ttpp) REVERT: D 268 LEU cc_start: 0.9206 (tp) cc_final: 0.8993 (tp) REVERT: D 366 LYS cc_start: 0.8870 (mppt) cc_final: 0.8400 (mmmt) REVERT: D 402 SER cc_start: 0.9070 (t) cc_final: 0.8853 (p) REVERT: D 431 MET cc_start: 0.8650 (ttm) cc_final: 0.8259 (ttm) REVERT: D 497 ILE cc_start: 0.9068 (tp) cc_final: 0.8766 (tt) REVERT: D 555 MET cc_start: 0.8151 (tpp) cc_final: 0.7848 (tpp) REVERT: D 561 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8755 (t0) REVERT: D 562 MET cc_start: 0.9095 (tpp) cc_final: 0.8804 (tpp) REVERT: D 595 ILE cc_start: 0.9357 (mm) cc_final: 0.8999 (tp) REVERT: D 740 THR cc_start: 0.7482 (m) cc_final: 0.7171 (t) outliers start: 8 outliers final: 4 residues processed: 512 average time/residue: 0.1132 time to fit residues: 94.0042 Evaluate side-chains 375 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 367 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 215 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 112 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.4253 > 50:) chunk 128 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS C 671 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095201 restraints weight = 40275.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097380 restraints weight = 25978.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098994 restraints weight = 18883.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100152 restraints weight = 14906.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100898 restraints weight = 12510.695| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19320 Z= 0.143 Angle : 0.651 9.970 26120 Z= 0.329 Chirality : 0.041 0.176 3000 Planarity : 0.005 0.066 3236 Dihedral : 4.627 21.916 2524 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2288 helix: -0.10 (0.14), residues: 1460 sheet: -0.94 (0.78), residues: 40 loop : -3.01 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.013 0.001 TYR A 661 PHE 0.018 0.001 PHE B 656 TRP 0.007 0.001 TRP D 380 HIS 0.004 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (19320) covalent geometry : angle 0.65062 / 0.33 (26120) hydrogen bonds : bond 0.04225 / 2.82 ( 996) hydrogen bonds : angle 4.08978 / 2.88 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 434 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7639 (ttpp) REVERT: A 366 LYS cc_start: 0.8844 (mppt) cc_final: 0.8340 (mmmt) REVERT: A 402 SER cc_start: 0.9088 (p) cc_final: 0.8778 (t) REVERT: A 527 PHE cc_start: 0.8252 (t80) cc_final: 0.7849 (t80) REVERT: A 555 MET cc_start: 0.8250 (tpp) cc_final: 0.7855 (tpp) REVERT: A 562 MET cc_start: 0.9037 (tpp) cc_final: 0.8831 (tpp) REVERT: A 592 PHE cc_start: 0.8764 (t80) cc_final: 0.8525 (t80) REVERT: A 595 ILE cc_start: 0.9370 (mm) cc_final: 0.9040 (tp) REVERT: A 677 MET cc_start: 0.8079 (ttt) cc_final: 0.7869 (tpp) REVERT: A 740 THR cc_start: 0.7495 (m) cc_final: 0.7235 (p) REVERT: B 246 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7586 (ttpp) REVERT: B 268 LEU cc_start: 0.9265 (tp) cc_final: 0.9064 (tp) REVERT: B 366 LYS cc_start: 0.8871 (mppt) cc_final: 0.8377 (mmmt) REVERT: B 402 SER cc_start: 0.9058 (t) cc_final: 0.8826 (p) REVERT: B 527 PHE cc_start: 0.8218 (t80) cc_final: 0.7985 (t80) REVERT: B 562 MET cc_start: 0.9094 (tpp) cc_final: 0.8860 (tpp) REVERT: B 575 TYR cc_start: 0.8301 (t80) cc_final: 0.8030 (t80) REVERT: B 592 PHE cc_start: 0.8769 (t80) cc_final: 0.8550 (t80) REVERT: B 595 ILE cc_start: 0.9381 (mm) cc_final: 0.9043 (tp) REVERT: B 740 THR cc_start: 0.7484 (m) cc_final: 0.7246 (p) REVERT: C 174 LYS cc_start: 0.8974 (tptt) cc_final: 0.8509 (tptt) REVERT: C 205 ASN cc_start: 0.8625 (m-40) cc_final: 0.8419 (p0) REVERT: C 246 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7571 (ttpp) REVERT: C 268 LEU cc_start: 0.9275 (tp) cc_final: 0.9075 (tp) REVERT: C 366 LYS cc_start: 0.8894 (mppt) cc_final: 0.8450 (mmmt) REVERT: C 402 SER cc_start: 0.9056 (t) cc_final: 0.8793 (p) REVERT: C 527 PHE cc_start: 0.8279 (t80) cc_final: 0.8040 (t80) REVERT: C 562 MET cc_start: 0.9064 (tpp) cc_final: 0.8841 (tpp) REVERT: C 592 PHE cc_start: 0.8787 (t80) cc_final: 0.8538 (t80) REVERT: C 595 ILE cc_start: 0.9352 (mm) cc_final: 0.9027 (tp) REVERT: D 246 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7604 (ttpp) REVERT: D 268 LEU cc_start: 0.9235 (tp) cc_final: 0.8993 (tp) REVERT: D 366 LYS cc_start: 0.8844 (mppt) cc_final: 0.8391 (mmmt) REVERT: D 402 SER cc_start: 0.9077 (t) cc_final: 0.8829 (p) REVERT: D 527 PHE cc_start: 0.8292 (t80) cc_final: 0.8041 (t80) REVERT: D 555 MET cc_start: 0.8274 (tpp) cc_final: 0.7876 (tpp) REVERT: D 562 MET cc_start: 0.9096 (tpp) cc_final: 0.8840 (tpp) REVERT: D 575 TYR cc_start: 0.8306 (t80) cc_final: 0.8062 (t80) REVERT: D 592 PHE cc_start: 0.8778 (t80) cc_final: 0.8529 (t80) REVERT: D 595 ILE cc_start: 0.9379 (mm) cc_final: 0.9055 (tp) REVERT: D 716 ARG cc_start: 0.8604 (mmp80) cc_final: 0.8291 (mmp80) REVERT: D 740 THR cc_start: 0.7434 (m) cc_final: 0.7203 (p) outliers start: 1 outliers final: 0 residues processed: 435 average time/residue: 0.1154 time to fit residues: 80.7480 Evaluate side-chains 358 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 181 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 129 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 570 GLN A 671 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 561 ASN B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 561 ASN C 671 ASN C 683 ASN ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN D 671 ASN D 683 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092202 restraints weight = 40986.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094341 restraints weight = 26234.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095836 restraints weight = 19034.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096956 restraints weight = 15076.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097583 restraints weight = 12680.896| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19320 Z= 0.186 Angle : 0.695 9.767 26120 Z= 0.352 Chirality : 0.043 0.188 3000 Planarity : 0.005 0.073 3236 Dihedral : 4.638 22.483 2524 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2288 helix: 0.07 (0.13), residues: 1472 sheet: -2.40 (0.57), residues: 64 loop : -2.85 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 716 TYR 0.012 0.001 TYR B 661 PHE 0.023 0.002 PHE D 656 TRP 0.009 0.001 TRP B 380 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (19320) covalent geometry : angle 0.69504 / 0.35 (26120) hydrogen bonds : bond 0.04455 / 2.98 ( 996) hydrogen bonds : angle 4.21457 / 2.96 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7685 (ttpp) REVERT: A 366 LYS cc_start: 0.8845 (mppt) cc_final: 0.8418 (mmmt) REVERT: A 402 SER cc_start: 0.9082 (p) cc_final: 0.8746 (t) REVERT: A 501 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 527 PHE cc_start: 0.8354 (t80) cc_final: 0.8066 (t80) REVERT: A 562 MET cc_start: 0.8998 (tpp) cc_final: 0.8772 (tpp) REVERT: A 592 PHE cc_start: 0.8836 (t80) cc_final: 0.8605 (t80) REVERT: A 595 ILE cc_start: 0.9411 (mm) cc_final: 0.9082 (tp) REVERT: A 688 SER cc_start: 0.9121 (p) cc_final: 0.8277 (p) REVERT: B 246 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7691 (ttpp) REVERT: B 268 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tp) REVERT: B 366 LYS cc_start: 0.8896 (mppt) cc_final: 0.8330 (mmmt) REVERT: B 501 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 527 PHE cc_start: 0.8368 (t80) cc_final: 0.8074 (t80) REVERT: B 562 MET cc_start: 0.9074 (tpp) cc_final: 0.8844 (tpp) REVERT: B 592 PHE cc_start: 0.8853 (t80) cc_final: 0.8612 (t80) REVERT: B 595 ILE cc_start: 0.9410 (mm) cc_final: 0.9058 (tp) REVERT: C 205 ASN cc_start: 0.8761 (m-40) cc_final: 0.8425 (p0) REVERT: C 246 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7672 (ttpp) REVERT: C 268 LEU cc_start: 0.9236 (tp) cc_final: 0.9033 (tp) REVERT: C 366 LYS cc_start: 0.8894 (mppt) cc_final: 0.8382 (mmmt) REVERT: C 501 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 527 PHE cc_start: 0.8410 (t80) cc_final: 0.8192 (t80) REVERT: C 562 MET cc_start: 0.9066 (tpp) cc_final: 0.8832 (tpp) REVERT: C 592 PHE cc_start: 0.8862 (t80) cc_final: 0.8621 (t80) REVERT: C 595 ILE cc_start: 0.9398 (mm) cc_final: 0.9048 (tp) REVERT: D 246 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7672 (ttpp) REVERT: D 268 LEU cc_start: 0.9211 (tp) cc_final: 0.8980 (tp) REVERT: D 366 LYS cc_start: 0.8852 (mppt) cc_final: 0.8333 (mmmt) REVERT: D 501 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8080 (mm-30) REVERT: D 527 PHE cc_start: 0.8417 (t80) cc_final: 0.8195 (t80) REVERT: D 555 MET cc_start: 0.8347 (tpp) cc_final: 0.8071 (tpp) REVERT: D 562 MET cc_start: 0.9065 (tpp) cc_final: 0.8836 (tpp) REVERT: D 592 PHE cc_start: 0.8850 (t80) cc_final: 0.8607 (t80) REVERT: D 595 ILE cc_start: 0.9399 (mm) cc_final: 0.9036 (tp) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1283 time to fit residues: 79.6366 Evaluate side-chains 338 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 125 optimal weight: 0.0770 chunk 111 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 671 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096955 restraints weight = 39802.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099313 restraints weight = 25081.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100924 restraints weight = 17789.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102165 restraints weight = 13884.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102941 restraints weight = 11531.763| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19320 Z= 0.122 Angle : 0.659 10.181 26120 Z= 0.325 Chirality : 0.040 0.167 3000 Planarity : 0.005 0.061 3236 Dihedral : 4.428 22.948 2524 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.18), residues: 2288 helix: 0.30 (0.14), residues: 1484 sheet: -0.83 (0.79), residues: 40 loop : -2.95 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 690 TYR 0.014 0.001 TYR B 575 PHE 0.015 0.001 PHE B 442 TRP 0.013 0.001 TRP C 493 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (19320) covalent geometry : angle 0.65940 / 0.33 (26120) hydrogen bonds : bond 0.03797 / 2.56 ( 996) hydrogen bonds : angle 3.95426 / 2.80 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8938 (tptt) cc_final: 0.8506 (mmmt) REVERT: A 233 LEU cc_start: 0.9295 (pp) cc_final: 0.8881 (tt) REVERT: A 366 LYS cc_start: 0.8839 (mppt) cc_final: 0.8380 (mmmt) REVERT: A 402 SER cc_start: 0.8938 (p) cc_final: 0.8718 (t) REVERT: A 501 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 562 MET cc_start: 0.8948 (tpp) cc_final: 0.8644 (tpp) REVERT: A 572 MET cc_start: 0.8419 (tpp) cc_final: 0.8213 (tpp) REVERT: A 574 MET cc_start: 0.8679 (mmt) cc_final: 0.8366 (mmt) REVERT: A 575 TYR cc_start: 0.8187 (t80) cc_final: 0.7965 (t80) REVERT: A 595 ILE cc_start: 0.9363 (mm) cc_final: 0.9050 (tp) REVERT: B 174 LYS cc_start: 0.8910 (tptt) cc_final: 0.8426 (tptt) REVERT: B 178 ASN cc_start: 0.8644 (m110) cc_final: 0.8386 (m-40) REVERT: B 246 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7621 (ttpp) REVERT: B 285 GLU cc_start: 0.8366 (pt0) cc_final: 0.7691 (pp20) REVERT: B 366 LYS cc_start: 0.8850 (mppt) cc_final: 0.8415 (mmmt) REVERT: B 402 SER cc_start: 0.8987 (t) cc_final: 0.8717 (p) REVERT: B 501 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 562 MET cc_start: 0.8998 (tpp) cc_final: 0.8766 (tpp) REVERT: B 574 MET cc_start: 0.8744 (mmt) cc_final: 0.8412 (mmt) REVERT: B 592 PHE cc_start: 0.8781 (t80) cc_final: 0.8570 (t80) REVERT: B 595 ILE cc_start: 0.9363 (mm) cc_final: 0.9046 (tp) REVERT: C 159 MET cc_start: 0.6519 (mpp) cc_final: 0.6275 (mpp) REVERT: C 174 LYS cc_start: 0.8958 (tptt) cc_final: 0.8505 (tptt) REVERT: C 233 LEU cc_start: 0.9247 (pp) cc_final: 0.8852 (tt) REVERT: C 246 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7614 (ttpp) REVERT: C 323 MET cc_start: 0.8922 (tmm) cc_final: 0.8706 (tmm) REVERT: C 366 LYS cc_start: 0.8882 (mppt) cc_final: 0.8467 (mmmt) REVERT: C 402 SER cc_start: 0.9003 (t) cc_final: 0.8715 (p) REVERT: C 501 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7905 (tp30) REVERT: C 527 PHE cc_start: 0.8219 (t80) cc_final: 0.7948 (t80) REVERT: C 562 MET cc_start: 0.8972 (tpp) cc_final: 0.8651 (tpp) REVERT: C 592 PHE cc_start: 0.8812 (t80) cc_final: 0.8555 (t80) REVERT: D 174 LYS cc_start: 0.8934 (tptt) cc_final: 0.8423 (tptt) REVERT: D 178 ASN cc_start: 0.8683 (m110) cc_final: 0.8449 (m110) REVERT: D 233 LEU cc_start: 0.9258 (pp) cc_final: 0.8858 (tt) REVERT: D 246 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7622 (ttpp) REVERT: D 285 GLU cc_start: 0.8339 (pt0) cc_final: 0.7747 (pp20) REVERT: D 366 LYS cc_start: 0.8848 (mppt) cc_final: 0.8415 (mmmt) REVERT: D 402 SER cc_start: 0.8957 (t) cc_final: 0.8661 (p) REVERT: D 501 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8026 (mm-30) REVERT: D 527 PHE cc_start: 0.8265 (t80) cc_final: 0.7992 (t80) REVERT: D 592 PHE cc_start: 0.8760 (t80) cc_final: 0.8528 (t80) REVERT: D 595 ILE cc_start: 0.9363 (mm) cc_final: 0.9050 (tp) outliers start: 2 outliers final: 0 residues processed: 481 average time/residue: 0.1159 time to fit residues: 89.4297 Evaluate side-chains 354 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 168 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 242 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 671 ASN D 242 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096114 restraints weight = 39849.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098415 restraints weight = 25508.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100049 restraints weight = 18414.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101231 restraints weight = 14481.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102076 restraints weight = 12134.196| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19320 Z= 0.122 Angle : 0.668 10.032 26120 Z= 0.326 Chirality : 0.040 0.179 3000 Planarity : 0.004 0.059 3236 Dihedral : 4.250 22.478 2524 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.15 % Allowed : 3.10 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2288 helix: 0.44 (0.14), residues: 1480 sheet: -1.77 (0.57), residues: 64 loop : -2.71 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 716 TYR 0.013 0.001 TYR D 575 PHE 0.017 0.001 PHE B 656 TRP 0.007 0.001 TRP B 380 HIS 0.003 0.000 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (19320) covalent geometry : angle 0.66752 / 0.33 (26120) hydrogen bonds : bond 0.03779 / 2.52 ( 996) hydrogen bonds : angle 3.89199 / 2.75 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 455 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8934 (tptt) cc_final: 0.8409 (tptt) REVERT: A 178 ASN cc_start: 0.8668 (m110) cc_final: 0.8373 (m110) REVERT: A 233 LEU cc_start: 0.9248 (pp) cc_final: 0.8884 (tt) REVERT: A 366 LYS cc_start: 0.8829 (mppt) cc_final: 0.8336 (mmmt) REVERT: A 555 MET cc_start: 0.8076 (tpp) cc_final: 0.7852 (tpp) REVERT: A 562 MET cc_start: 0.9038 (tpp) cc_final: 0.8620 (tpp) REVERT: A 595 ILE cc_start: 0.9374 (mm) cc_final: 0.9085 (tp) REVERT: A 717 MET cc_start: 0.7886 (tmm) cc_final: 0.7524 (ttt) REVERT: B 174 LYS cc_start: 0.8944 (tptt) cc_final: 0.8447 (tptt) REVERT: B 178 ASN cc_start: 0.8675 (m110) cc_final: 0.8385 (m-40) REVERT: B 246 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7621 (ttpp) REVERT: B 285 GLU cc_start: 0.8409 (pt0) cc_final: 0.7803 (pp20) REVERT: B 366 LYS cc_start: 0.8874 (mppt) cc_final: 0.8406 (mmmt) REVERT: B 402 SER cc_start: 0.8964 (t) cc_final: 0.8686 (p) REVERT: B 501 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7793 (tm-30) REVERT: B 595 ILE cc_start: 0.9360 (mm) cc_final: 0.9077 (tp) REVERT: C 159 MET cc_start: 0.6652 (mpp) cc_final: 0.6356 (mpp) REVERT: C 174 LYS cc_start: 0.8936 (tptt) cc_final: 0.8411 (tptt) REVERT: C 178 ASN cc_start: 0.8714 (m110) cc_final: 0.8440 (m110) REVERT: C 233 LEU cc_start: 0.9245 (pp) cc_final: 0.8873 (tt) REVERT: C 246 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7604 (ttpp) REVERT: C 366 LYS cc_start: 0.8917 (mppt) cc_final: 0.8455 (mmmt) REVERT: C 402 SER cc_start: 0.9022 (t) cc_final: 0.8695 (p) REVERT: C 501 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8044 (mm-30) REVERT: C 527 PHE cc_start: 0.8275 (t80) cc_final: 0.8030 (t80) REVERT: C 562 MET cc_start: 0.9090 (tpp) cc_final: 0.8852 (tpp) REVERT: C 595 ILE cc_start: 0.9368 (mm) cc_final: 0.9067 (tp) REVERT: C 743 LYS cc_start: 0.7932 (mttt) cc_final: 0.7675 (mmtp) REVERT: D 174 LYS cc_start: 0.8956 (tptt) cc_final: 0.8413 (tptt) REVERT: D 178 ASN cc_start: 0.8681 (m110) cc_final: 0.8383 (m110) REVERT: D 233 LEU cc_start: 0.9239 (pp) cc_final: 0.8881 (tt) REVERT: D 246 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7608 (ttpp) REVERT: D 285 GLU cc_start: 0.8354 (pt0) cc_final: 0.7740 (pp20) REVERT: D 366 LYS cc_start: 0.8842 (mppt) cc_final: 0.8398 (mmmt) REVERT: D 402 SER cc_start: 0.8991 (t) cc_final: 0.8684 (p) REVERT: D 501 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8037 (mm-30) REVERT: D 527 PHE cc_start: 0.8281 (t80) cc_final: 0.8026 (t80) REVERT: D 555 MET cc_start: 0.8245 (tpp) cc_final: 0.7850 (tpp) REVERT: D 595 ILE cc_start: 0.9364 (mm) cc_final: 0.9064 (tp) REVERT: D 688 SER cc_start: 0.9111 (p) cc_final: 0.8011 (p) outliers start: 3 outliers final: 0 residues processed: 458 average time/residue: 0.1133 time to fit residues: 84.3963 Evaluate side-chains 366 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 212 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 180 optimal weight: 0.0060 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 683 ASN B 273 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 671 ASN B 683 ASN C 242 ASN C 273 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 671 ASN D 273 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 671 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097340 restraints weight = 40176.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099636 restraints weight = 25699.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101305 restraints weight = 18514.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102366 restraints weight = 14475.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103248 restraints weight = 12226.625| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19320 Z= 0.116 Angle : 0.662 10.026 26120 Z= 0.322 Chirality : 0.040 0.167 3000 Planarity : 0.004 0.058 3236 Dihedral : 4.168 21.801 2524 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.15 % Allowed : 2.46 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2288 helix: 0.62 (0.14), residues: 1476 sheet: -1.53 (0.57), residues: 64 loop : -2.66 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 716 TYR 0.012 0.001 TYR B 575 PHE 0.021 0.001 PHE B 442 TRP 0.016 0.001 TRP C 493 HIS 0.002 0.000 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (19320) covalent geometry : angle 0.66190 / 0.32 (26120) hydrogen bonds : bond 0.03617 / 2.42 ( 996) hydrogen bonds : angle 3.82867 / 2.71 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 460 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8916 (tptt) cc_final: 0.8362 (tptt) REVERT: A 178 ASN cc_start: 0.8659 (m110) cc_final: 0.8391 (m110) REVERT: A 233 LEU cc_start: 0.9265 (pp) cc_final: 0.8893 (tt) REVERT: A 366 LYS cc_start: 0.8821 (mppt) cc_final: 0.8351 (mmmt) REVERT: A 562 MET cc_start: 0.9033 (tpp) cc_final: 0.8676 (tpp) REVERT: A 574 MET cc_start: 0.8563 (mmt) cc_final: 0.8215 (mmt) REVERT: A 668 LEU cc_start: 0.9338 (tp) cc_final: 0.8918 (tp) REVERT: A 739 TRP cc_start: 0.7583 (m100) cc_final: 0.7370 (m100) REVERT: A 743 LYS cc_start: 0.7766 (mttt) cc_final: 0.7527 (mmtt) REVERT: B 174 LYS cc_start: 0.8940 (tptt) cc_final: 0.8443 (tptt) REVERT: B 178 ASN cc_start: 0.8726 (m110) cc_final: 0.8406 (m-40) REVERT: B 233 LEU cc_start: 0.9239 (pp) cc_final: 0.8854 (tt) REVERT: B 366 LYS cc_start: 0.8865 (mppt) cc_final: 0.8386 (mmmt) REVERT: B 402 SER cc_start: 0.8943 (t) cc_final: 0.8690 (p) REVERT: B 574 MET cc_start: 0.8558 (mmt) cc_final: 0.8201 (mmt) REVERT: B 575 TYR cc_start: 0.8097 (t80) cc_final: 0.7877 (t80) REVERT: B 595 ILE cc_start: 0.9371 (mm) cc_final: 0.9071 (tp) REVERT: C 159 MET cc_start: 0.6709 (mpp) cc_final: 0.6358 (mpp) REVERT: C 174 LYS cc_start: 0.8928 (tptt) cc_final: 0.8406 (tptt) REVERT: C 178 ASN cc_start: 0.8747 (m110) cc_final: 0.8456 (m110) REVERT: C 233 LEU cc_start: 0.9213 (pp) cc_final: 0.8850 (tt) REVERT: C 246 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7564 (ttpp) REVERT: C 366 LYS cc_start: 0.8883 (mppt) cc_final: 0.8442 (mmmt) REVERT: C 402 SER cc_start: 0.8974 (t) cc_final: 0.8652 (p) REVERT: C 527 PHE cc_start: 0.8252 (t80) cc_final: 0.8034 (t80) REVERT: D 174 LYS cc_start: 0.8962 (tptt) cc_final: 0.8462 (tptt) REVERT: D 178 ASN cc_start: 0.8740 (m110) cc_final: 0.8408 (m-40) REVERT: D 233 LEU cc_start: 0.9231 (pp) cc_final: 0.8871 (tt) REVERT: D 366 LYS cc_start: 0.8839 (mppt) cc_final: 0.8387 (mmmt) REVERT: D 402 SER cc_start: 0.8958 (t) cc_final: 0.8678 (p) REVERT: D 555 MET cc_start: 0.8052 (tpp) cc_final: 0.7803 (tpp) outliers start: 3 outliers final: 0 residues processed: 463 average time/residue: 0.1145 time to fit residues: 85.6725 Evaluate side-chains 348 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 0.0980 chunk 208 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 242 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 671 ASN D 242 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097132 restraints weight = 40298.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099533 restraints weight = 26118.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101164 restraints weight = 18659.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102330 restraints weight = 14610.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103189 restraints weight = 12207.127| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19320 Z= 0.124 Angle : 0.687 11.453 26120 Z= 0.332 Chirality : 0.041 0.166 3000 Planarity : 0.004 0.058 3236 Dihedral : 4.155 21.271 2524 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2288 helix: 0.69 (0.14), residues: 1476 sheet: -1.43 (0.58), residues: 64 loop : -2.57 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 567 TYR 0.014 0.001 TYR C 650 PHE 0.021 0.001 PHE A 538 TRP 0.016 0.001 TRP D 493 HIS 0.002 0.000 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19320) covalent geometry : angle 0.68687 / 0.33 (26120) hydrogen bonds : bond 0.03672 / 2.46 ( 996) hydrogen bonds : angle 3.84966 / 2.72 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 445 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8916 (tptt) cc_final: 0.8329 (tptt) REVERT: A 178 ASN cc_start: 0.8627 (m110) cc_final: 0.8284 (m110) REVERT: A 366 LYS cc_start: 0.8829 (mppt) cc_final: 0.8344 (mmmt) REVERT: A 527 PHE cc_start: 0.8197 (t80) cc_final: 0.7840 (t80) REVERT: A 562 MET cc_start: 0.9036 (tpp) cc_final: 0.8822 (tpp) REVERT: A 575 TYR cc_start: 0.8122 (t80) cc_final: 0.7884 (t80) REVERT: A 668 LEU cc_start: 0.9320 (tp) cc_final: 0.8857 (tp) REVERT: A 694 LEU cc_start: 0.9327 (mm) cc_final: 0.8875 (tt) REVERT: B 174 LYS cc_start: 0.8957 (tptt) cc_final: 0.8426 (tptt) REVERT: B 178 ASN cc_start: 0.8683 (m110) cc_final: 0.8346 (m-40) REVERT: B 233 LEU cc_start: 0.9252 (pp) cc_final: 0.8851 (tt) REVERT: B 366 LYS cc_start: 0.8862 (mppt) cc_final: 0.8375 (mmmt) REVERT: B 402 SER cc_start: 0.8925 (t) cc_final: 0.8668 (p) REVERT: B 527 PHE cc_start: 0.8169 (t80) cc_final: 0.7826 (t80) REVERT: B 575 TYR cc_start: 0.8095 (t80) cc_final: 0.7795 (t80) REVERT: C 159 MET cc_start: 0.6584 (mpp) cc_final: 0.6251 (mpp) REVERT: C 174 LYS cc_start: 0.8914 (tptt) cc_final: 0.8416 (tptt) REVERT: C 178 ASN cc_start: 0.8716 (m110) cc_final: 0.8417 (m-40) REVERT: C 233 LEU cc_start: 0.9221 (pp) cc_final: 0.8872 (tt) REVERT: C 366 LYS cc_start: 0.8877 (mppt) cc_final: 0.8419 (mmmt) REVERT: C 402 SER cc_start: 0.8936 (t) cc_final: 0.8660 (p) REVERT: C 527 PHE cc_start: 0.8266 (t80) cc_final: 0.8045 (t80) REVERT: C 592 PHE cc_start: 0.8854 (t80) cc_final: 0.8626 (t80) REVERT: C 717 MET cc_start: 0.7870 (tmm) cc_final: 0.7245 (ttt) REVERT: C 743 LYS cc_start: 0.7910 (mttt) cc_final: 0.7675 (mmtp) REVERT: D 174 LYS cc_start: 0.8948 (tptt) cc_final: 0.8432 (tptt) REVERT: D 178 ASN cc_start: 0.8583 (m110) cc_final: 0.8276 (m-40) REVERT: D 233 LEU cc_start: 0.9231 (pp) cc_final: 0.8864 (tt) REVERT: D 366 LYS cc_start: 0.8846 (mppt) cc_final: 0.8383 (mmmt) REVERT: D 402 SER cc_start: 0.8959 (t) cc_final: 0.8658 (p) REVERT: D 555 MET cc_start: 0.7975 (tpp) cc_final: 0.7665 (tpp) REVERT: D 668 LEU cc_start: 0.9310 (tp) cc_final: 0.8903 (tp) REVERT: D 694 LEU cc_start: 0.9308 (mm) cc_final: 0.8896 (tt) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.1122 time to fit residues: 82.2827 Evaluate side-chains 352 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 150 optimal weight: 0.0070 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 671 ASN B 242 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 242 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098416 restraints weight = 39668.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100743 restraints weight = 25467.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102355 restraints weight = 18344.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103547 restraints weight = 14445.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104382 restraints weight = 12095.515| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19320 Z= 0.119 Angle : 0.693 10.462 26120 Z= 0.334 Chirality : 0.040 0.159 3000 Planarity : 0.004 0.059 3236 Dihedral : 4.105 20.715 2524 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2288 helix: 0.69 (0.14), residues: 1472 sheet: -1.34 (0.58), residues: 64 loop : -2.53 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 716 TYR 0.015 0.001 TYR A 650 PHE 0.018 0.001 PHE B 715 TRP 0.014 0.001 TRP A 493 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (19320) covalent geometry : angle 0.69264 / 0.33 (26120) hydrogen bonds : bond 0.03568 / 2.39 ( 996) hydrogen bonds : angle 3.81969 / 2.70 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8931 (tptt) cc_final: 0.8315 (tptt) REVERT: A 178 ASN cc_start: 0.8670 (m110) cc_final: 0.8353 (m110) REVERT: A 366 LYS cc_start: 0.8844 (mppt) cc_final: 0.8300 (mmmt) REVERT: A 527 PHE cc_start: 0.8123 (t80) cc_final: 0.7786 (t80) REVERT: A 668 LEU cc_start: 0.9274 (tp) cc_final: 0.8799 (tp) REVERT: A 694 LEU cc_start: 0.9288 (mm) cc_final: 0.8849 (tt) REVERT: B 174 LYS cc_start: 0.8937 (tptt) cc_final: 0.8406 (tptt) REVERT: B 178 ASN cc_start: 0.8598 (m110) cc_final: 0.8288 (m-40) REVERT: B 366 LYS cc_start: 0.8874 (mppt) cc_final: 0.8362 (mmmt) REVERT: C 159 MET cc_start: 0.6641 (mpp) cc_final: 0.6277 (mpp) REVERT: C 174 LYS cc_start: 0.8920 (tptt) cc_final: 0.8417 (tptt) REVERT: C 178 ASN cc_start: 0.8726 (m110) cc_final: 0.8406 (m-40) REVERT: C 366 LYS cc_start: 0.8907 (mppt) cc_final: 0.8411 (mmmt) REVERT: C 402 SER cc_start: 0.8862 (t) cc_final: 0.8591 (p) REVERT: C 527 PHE cc_start: 0.8231 (t80) cc_final: 0.7995 (t80) REVERT: C 717 MET cc_start: 0.7891 (tmm) cc_final: 0.7344 (ttt) REVERT: D 174 LYS cc_start: 0.8955 (tptt) cc_final: 0.8413 (tptt) REVERT: D 178 ASN cc_start: 0.8594 (m110) cc_final: 0.8267 (m-40) REVERT: D 366 LYS cc_start: 0.8829 (mppt) cc_final: 0.8346 (mmmt) REVERT: D 402 SER cc_start: 0.8883 (t) cc_final: 0.8623 (p) REVERT: D 555 MET cc_start: 0.7969 (tpp) cc_final: 0.7622 (tpp) REVERT: D 668 LEU cc_start: 0.9260 (tp) cc_final: 0.8868 (tp) REVERT: D 694 LEU cc_start: 0.9289 (mm) cc_final: 0.8871 (tt) REVERT: D 740 THR cc_start: 0.7638 (m) cc_final: 0.7435 (p) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1095 time to fit residues: 79.3898 Evaluate side-chains 354 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 205 optimal weight: 0.6980 chunk 138 optimal weight: 0.0060 chunk 144 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 228 optimal weight: 0.0770 chunk 179 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 671 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100048 restraints weight = 39335.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102383 restraints weight = 25349.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104012 restraints weight = 18267.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105219 restraints weight = 14372.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106077 restraints weight = 12001.458| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19320 Z= 0.118 Angle : 0.696 9.819 26120 Z= 0.332 Chirality : 0.040 0.160 3000 Planarity : 0.004 0.059 3236 Dihedral : 4.006 19.306 2524 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.05 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2288 helix: 0.77 (0.14), residues: 1484 sheet: -1.16 (0.59), residues: 64 loop : -2.60 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 716 TYR 0.014 0.001 TYR A 650 PHE 0.023 0.001 PHE C 538 TRP 0.014 0.001 TRP C 493 HIS 0.002 0.000 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (19320) covalent geometry : angle 0.69619 / 0.33 (26120) hydrogen bonds : bond 0.03448 / 2.31 ( 996) hydrogen bonds : angle 3.79340 / 2.68 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4576 Ramachandran restraints generated. 2288 Oldfield, 0 Emsley, 2288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8932 (tptt) cc_final: 0.8619 (tptp) REVERT: A 233 LEU cc_start: 0.9260 (pp) cc_final: 0.8912 (tt) REVERT: A 366 LYS cc_start: 0.8849 (mppt) cc_final: 0.8263 (mmmt) REVERT: A 527 PHE cc_start: 0.8097 (t80) cc_final: 0.7784 (t80) REVERT: A 574 MET cc_start: 0.8347 (mmt) cc_final: 0.8094 (mmt) REVERT: A 592 PHE cc_start: 0.8776 (t80) cc_final: 0.8565 (t80) REVERT: A 668 LEU cc_start: 0.9270 (tp) cc_final: 0.8956 (tp) REVERT: A 694 LEU cc_start: 0.9247 (mm) cc_final: 0.8794 (tt) REVERT: A 739 TRP cc_start: 0.7616 (m100) cc_final: 0.7362 (m100) REVERT: B 174 LYS cc_start: 0.8930 (tptt) cc_final: 0.8697 (tptp) REVERT: B 233 LEU cc_start: 0.9232 (pp) cc_final: 0.8888 (tt) REVERT: B 366 LYS cc_start: 0.8867 (mppt) cc_final: 0.8350 (mmmt) REVERT: C 174 LYS cc_start: 0.8916 (tptt) cc_final: 0.8407 (tptt) REVERT: C 178 ASN cc_start: 0.8640 (m110) cc_final: 0.8325 (m-40) REVERT: C 233 LEU cc_start: 0.9280 (pp) cc_final: 0.8946 (tt) REVERT: C 357 LEU cc_start: 0.9061 (tt) cc_final: 0.8465 (mp) REVERT: C 366 LYS cc_start: 0.8848 (mppt) cc_final: 0.8384 (mmmt) REVERT: C 668 LEU cc_start: 0.9232 (tp) cc_final: 0.8877 (tp) REVERT: C 743 LYS cc_start: 0.7929 (mttt) cc_final: 0.7680 (mmtp) REVERT: D 174 LYS cc_start: 0.8922 (tptt) cc_final: 0.8663 (tptp) REVERT: D 233 LEU cc_start: 0.9214 (pp) cc_final: 0.8862 (tt) REVERT: D 357 LEU cc_start: 0.9062 (tt) cc_final: 0.8621 (mt) REVERT: D 366 LYS cc_start: 0.8853 (mppt) cc_final: 0.8326 (mmmt) REVERT: D 555 MET cc_start: 0.7840 (tpp) cc_final: 0.7514 (tpp) REVERT: D 668 LEU cc_start: 0.9291 (tp) cc_final: 0.9020 (tp) REVERT: D 694 LEU cc_start: 0.9228 (mm) cc_final: 0.8798 (tt) outliers start: 1 outliers final: 1 residues processed: 450 average time/residue: 0.1111 time to fit residues: 81.8725 Evaluate side-chains 360 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 115 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 671 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096459 restraints weight = 40047.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098691 restraints weight = 25867.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100300 restraints weight = 18616.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101425 restraints weight = 14679.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102196 restraints weight = 12333.515| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19320 Z= 0.139 Angle : 0.708 11.057 26120 Z= 0.345 Chirality : 0.042 0.166 3000 Planarity : 0.005 0.057 3236 Dihedral : 4.078 19.805 2524 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2288 helix: 0.81 (0.14), residues: 1480 sheet: -1.18 (0.61), residues: 64 loop : -2.49 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 716 TYR 0.015 0.001 TYR A 650 PHE 0.025 0.001 PHE D 527 TRP 0.015 0.001 TRP A 739 HIS 0.002 0.000 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (19320) covalent geometry : angle 0.70760 / 0.34 (26120) hydrogen bonds : bond 0.03746 / 2.49 ( 996) hydrogen bonds : angle 3.86911 / 2.73 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2815.81 seconds wall clock time: 49 minutes 42.46 seconds (2982.46 seconds total)