Starting phenix.real_space_refine on Sun May 3 16:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s8b_54658/05_2026/9s8b_54658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s8b_54658/05_2026/9s8b_54658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s8b_54658/05_2026/9s8b_54658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s8b_54658/05_2026/9s8b_54658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s8b_54658/05_2026/9s8b_54658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s8b_54658/05_2026/9s8b_54658.map" } resolution = 2.79 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 8885 2.51 5 N 2430 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14043 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 802, 6430 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 26, 'TRANS': 775} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 42 Conformer: "B" Number of residues, atoms: 802, 6430 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 26, 'TRANS': 775} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 6561 Chain: "B" Number of atoms: 6410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6410 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 774} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 591 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 4, 'HIP:plan-2': 1, 'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 571 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 81} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 19 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 19 " occ=0.50 Time building chain proxies: 5.00, per 1000 atoms: 0.36 Number of scatterers: 14043 At special positions: 0 Unit cell: (131.4, 126.801, 80.154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 2680 8.00 N 2430 7.00 C 8885 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: 1.14 Conformation dependent library (CDL) restraints added in 721.0 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 58.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 32 through 36 removed outlier: 3.785A pdb=" N ALA A 36 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.815A pdb=" N GLU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.736A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.574A pdb=" N ALA A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.942A pdb=" N VAL A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 306 Processing helix chain 'A' and resid 322 through 325 removed outlier: 3.517A pdb=" N VAL A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.531A pdb=" N GLN A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.820A pdb=" N ARG A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.247A pdb=" N GLN A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 536 removed outlier: 3.771A pdb=" N ASN A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 557 through 575 removed outlier: 4.073A pdb=" N ASN A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 614 removed outlier: 3.758A pdb=" N ASN A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 657 through 667 removed outlier: 4.062A pdb=" N MET A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 709 through 716 removed outlier: 4.119A pdb=" N TYR A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 759 through 775 Processing helix chain 'A' and resid 776 through 790 Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 795 through 807 removed outlier: 3.587A pdb=" N THR A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 Processing helix chain 'B' and resid 37 through 68 removed outlier: 3.789A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.511A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 removed outlier: 3.742A pdb=" N ARG B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 261 through 267 removed outlier: 4.010A pdb=" N VAL B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 266 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 306 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.557A pdb=" N GLN B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 371 through 378 Processing helix chain 'B' and resid 378 through 400 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 509 through 536 removed outlier: 4.081A pdb=" N ASN B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 575 removed outlier: 4.087A pdb=" N ASN B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 614 removed outlier: 3.651A pdb=" N ASN B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 658 through 667 Processing helix chain 'B' and resid 676 through 686 removed outlier: 4.481A pdb=" N GLU B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 709 through 717 removed outlier: 4.094A pdb=" N TYR B 713 " --> pdb=" O LYS B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 729 Processing helix chain 'B' and resid 740 through 749 Processing helix chain 'B' and resid 759 through 775 Processing helix chain 'B' and resid 776 through 790 Processing helix chain 'B' and resid 791 through 794 Processing helix chain 'B' and resid 795 through 807 removed outlier: 3.523A pdb=" N THR B 799 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 71 through 84 Processing helix chain 'D' and resid 15 through 27 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 71 through 84 removed outlier: 3.684A pdb=" N LEU D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 192 removed outlier: 3.955A pdb=" N ALA A 215 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 185 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N GLY A 213 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ARG A 187 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N ILE A 211 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS A 189 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N GLU A 209 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR A 230 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER A 355 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 317 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR A 357 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 319 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N ASN A 435 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 356 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 434 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.705A pdb=" N ARG A 420 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.349A pdb=" N ARG A 583 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 625 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN A 585 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP A 546 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY A 588 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN A 548 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 547 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 192 removed outlier: 12.683A pdb=" N LYS B 182 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 12.247A pdb=" N ILE B 219 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N HIS B 184 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 11.058A pdb=" N ASP B 217 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 186 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY B 144 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ARG B 232 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY B 146 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TRP B 234 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY B 148 " --> pdb=" O TRP B 234 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ALA B 236 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 72 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N TYR B 147 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR B 74 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ILE B 149 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 71 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N HIS B 318 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR B 73 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN B 320 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 75 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER B 355 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 317 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR B 357 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 319 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 433 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 434 " --> pdb=" O THR B 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB1, first strand: chain 'B' and resid 622 through 626 removed outlier: 6.374A pdb=" N ARG B 583 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL B 625 " --> pdb=" O ARG B 583 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN B 585 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 544 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE B 586 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 546 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY B 588 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN B 548 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE B 549 " --> pdb=" O GLU B 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 43 Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 7 removed outlier: 3.734A pdb=" N PHE D 2 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 65 " --> pdb=" O PHE D 2 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 32 " --> pdb=" O GLU D 66 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4695 1.34 - 1.46: 2848 1.46 - 1.58: 6685 1.58 - 1.69: 2 1.69 - 1.81: 83 Bond restraints: 14313 Sorted by residual: bond pdb=" ND1 HIP C 15 " pdb=" P HIP C 15 " ideal model delta sigma weight residual 1.928 1.703 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" NZ LLP B 662 " pdb=" C4' LLP B 662 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " ideal model delta sigma weight residual 1.273 1.428 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" OP4 LLP A 662 " pdb=" P LLP A 662 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" OP4 LLP B 662 " pdb=" P LLP B 662 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 14308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.17: 19441 8.17 - 16.35: 2 16.35 - 24.52: 2 24.52 - 32.69: 0 32.69 - 40.87: 1 Bond angle restraints: 19446 Sorted by residual: angle pdb=" CE LLP A 662 " pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " ideal model delta sigma weight residual 119.26 160.13 -40.87 3.00e+00 1.11e-01 1.86e+02 angle pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " pdb=" C4 LLP A 662 " ideal model delta sigma weight residual 120.09 141.52 -21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb=" NZ LLP B 662 " pdb=" C4' LLP B 662 " pdb=" C4 LLP B 662 " ideal model delta sigma weight residual 120.09 138.34 -18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" CA THR C 16 " pdb=" CB THR C 16 " pdb=" OG1 THR C 16 " ideal model delta sigma weight residual 109.60 103.09 6.51 1.50e+00 4.44e-01 1.88e+01 angle pdb=" ND1 HIP C 15 " pdb=" P HIP C 15 " pdb=" O1P HIP C 15 " ideal model delta sigma weight residual 98.03 109.88 -11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 19441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 8299 22.93 - 45.86: 183 45.86 - 68.78: 20 68.78 - 91.71: 3 91.71 - 114.64: 1 Dihedral angle restraints: 8506 sinusoidal: 3334 harmonic: 5172 Sorted by residual: dihedral pdb=" CD LLP A 662 " pdb=" CE LLP A 662 " pdb=" NZ LLP A 662 " pdb=" C4' LLP A 662 " ideal model delta sinusoidal sigma weight residual 249.72 135.08 114.64 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" CA GLN B 647 " pdb=" C GLN B 647 " pdb=" N ILE B 648 " pdb=" CA ILE B 648 " ideal model delta harmonic sigma weight residual 180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLN B 352 " pdb=" C GLN B 352 " pdb=" N VAL B 353 " pdb=" CA VAL B 353 " ideal model delta harmonic sigma weight residual 180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 8503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1265 0.027 - 0.054: 562 0.054 - 0.082: 211 0.082 - 0.109: 93 0.109 - 0.136: 32 Chirality restraints: 2163 Sorted by residual: chirality pdb=" CA PRO A 401 " pdb=" N PRO A 401 " pdb=" C PRO A 401 " pdb=" CB PRO A 401 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 220 " pdb=" N ILE A 220 " pdb=" C ILE A 220 " pdb=" CB ILE A 220 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO B 479 " pdb=" N PRO B 479 " pdb=" C PRO B 479 " pdb=" CB PRO B 479 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2160 not shown) Planarity restraints: 2527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 LLP B 662 " 0.011 2.00e-02 2.50e+03 6.96e-02 1.21e+02 pdb=" C2' LLP B 662 " 0.034 2.00e-02 2.50e+03 pdb=" C3 LLP B 662 " -0.045 2.00e-02 2.50e+03 pdb=" C4 LLP B 662 " -0.070 2.00e-02 2.50e+03 pdb=" C4' LLP B 662 " 0.165 2.00e-02 2.50e+03 pdb=" C5 LLP B 662 " -0.028 2.00e-02 2.50e+03 pdb=" C5' LLP B 662 " -0.057 2.00e-02 2.50e+03 pdb=" C6 LLP B 662 " 0.024 2.00e-02 2.50e+03 pdb=" N1 LLP B 662 " 0.045 2.00e-02 2.50e+03 pdb=" O3 LLP B 662 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 662 " -0.043 2.00e-02 2.50e+03 6.84e-02 4.69e+01 pdb=" NZ LLP A 662 " 0.102 2.00e-02 2.50e+03 pdb=" C4 LLP A 662 " 0.019 2.00e-02 2.50e+03 pdb=" C4' LLP A 662 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 662 " -0.028 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" NZ LLP B 662 " 0.017 2.00e-02 2.50e+03 pdb=" C4 LLP B 662 " -0.035 2.00e-02 2.50e+03 pdb=" C4' LLP B 662 " 0.047 2.00e-02 2.50e+03 ... (remaining 2524 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1588 2.75 - 3.28: 13711 3.28 - 3.82: 24309 3.82 - 4.36: 29280 4.36 - 4.90: 51293 Nonbonded interactions: 120181 Sorted by model distance: nonbonded pdb=" NH1 ARG A 70 " pdb=" O TRP A 808 " model vdw 2.207 3.120 nonbonded pdb=" O LEU A 474 " pdb=" OG SER A 482 " model vdw 2.208 3.040 nonbonded pdb=" O LEU B 474 " pdb=" OG SER B 482 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP A 414 " pdb=" OG SER A 416 " model vdw 2.220 3.040 nonbonded pdb=" O ALA A 238 " pdb=" OH TYR B 171 " model vdw 2.238 3.040 ... (remaining 120176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 18 or resid 20 through 272 or (resid 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 276 or ( \ resid 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 415 or (resid 416 through 417 and (name N or name CA or name C or name O \ or name CB )) or resid 418 through 454 or (resid 455 and (name N or name CA or \ name C or name O or name CB )) or resid 456 through 578 or (resid 579 and (name \ N or name CA or name C or name O or name CB )) or resid 580 through 715 or (resi \ d 716 and (name N or name CA or name C or name O or name CB )) or resid 717 thro \ ugh 734 or (resid 735 and (name N or name CA or name C or name O or name CB )) o \ r resid 736 through 813)) selection = (chain 'B' and (resid 13 through 18 or resid 20 through 223 or (resid 224 and (n \ ame N or name CA or name C or name O or name CB )) or resid 225 through 247 or ( \ resid 248 and (name N or name CA or name C or name O or name CB )) or resid 249 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 812 through 813)) } ncs_group { reference = (chain 'C' and (resid 1 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 or (resid 12 and (name N or name C \ A or name C or name O or name CB )) or resid 13 through 14 or resid 16 through 2 \ 6 or (resid 27 and (name N or name CA or name C or name O or name CB )) or resid \ 28 through 56 or (resid 57 and (name N or name CA or name C or name O or name C \ B )) or resid 58 through 70 or (resid 71 through 73 and (name N or name CA or na \ me C or name O or name CB )) or resid 74 or (resid 75 and (name N or name CA or \ name C or name O or name CB )) or resid 76 through 78 or (resid 79 and (name N o \ r name CA or name C or name O or name CB )) or resid 80 through 82 or (resid 83 \ and (name N or name CA or name C or name O or name CB )) or resid 84)) selection = (chain 'D' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 14 or resid 16 through 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB )) or resid 25 through 59 or (resid \ 60 and (name N or name CA or name C or name O or name CB )) or resid 61 through \ 69 or (resid 70 through 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 84)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.220 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 0.225 14313 Z= 0.233 Angle : 0.624 40.868 19446 Z= 0.291 Chirality : 0.039 0.136 2163 Planarity : 0.004 0.070 2527 Dihedral : 10.141 114.641 5176 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 1.09 % Allowed : 3.68 % Favored : 95.23 % 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: 1.01 (0.21), residues: 1758 helix: 1.59 (0.18), residues: 926 sheet: 0.15 (0.32), residues: 285 loop : -0.54 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 798 TYR 0.011 0.001 TYR B 569 PHE 0.016 0.002 PHE B 156 TRP 0.010 0.001 TRP A 473 HIS 0.007 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00485 (14313) covalent geometry : angle 0.62426 (19446) hydrogen bonds : bond 0.15453 ( 774) hydrogen bonds : angle 6.18515 ( 2200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.531 Fit side-chains REVERT: A 89 MET cc_start: 0.7637 (mtm) cc_final: 0.7393 (mtm) REVERT: B 89 MET cc_start: 0.7632 (mtm) cc_final: 0.7350 (mtm) REVERT: D 24 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8012 (ptpp) outliers start: 16 outliers final: 3 residues processed: 289 average time/residue: 0.5538 time to fit residues: 175.9267 Evaluate side-chains 154 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain D residue 24 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 249 GLN A 447 GLN A 492 ASN A 504 GLN A 660 ASN A 749 ASN B 447 GLN B 533 GLN B 534 GLN B 684 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.099731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079668 restraints weight = 45396.605| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.70 r_work: 0.3039 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14313 Z= 0.161 Angle : 0.570 10.524 19446 Z= 0.300 Chirality : 0.042 0.235 2163 Planarity : 0.004 0.043 2527 Dihedral : 6.014 81.177 1959 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 2.72 % Allowed : 10.42 % Favored : 86.85 % 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: 0.98 (0.21), residues: 1758 helix: 1.53 (0.17), residues: 936 sheet: 0.09 (0.31), residues: 283 loop : -0.50 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 204 TYR 0.025 0.001 TYR B 287 PHE 0.013 0.002 PHE A 392 TRP 0.017 0.001 TRP A 473 HIS 0.009 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00367 (14313) covalent geometry : angle 0.57041 (19446) hydrogen bonds : bond 0.04205 ( 774) hydrogen bonds : angle 4.98901 ( 2200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8048 (mp0) REVERT: A 89 MET cc_start: 0.8127 (mtm) cc_final: 0.7910 (mtm) REVERT: B 89 MET cc_start: 0.8199 (mtm) cc_final: 0.7916 (mtm) REVERT: B 155 MET cc_start: 0.8441 (ttp) cc_final: 0.8072 (ttt) REVERT: B 610 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8701 (ttmm) REVERT: C 45 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8223 (mmpt) REVERT: C 71 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8290 (tp-100) REVERT: C 75 GLU cc_start: 0.9033 (pt0) cc_final: 0.8654 (pt0) REVERT: D 21 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7136 (mm-40) REVERT: D 24 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7762 (ptpp) REVERT: D 49 LYS cc_start: 0.8828 (mttm) cc_final: 0.8624 (mttm) outliers start: 40 outliers final: 16 residues processed: 185 average time/residue: 0.5200 time to fit residues: 106.8613 Evaluate side-chains 159 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN C 76 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079392 restraints weight = 37211.905| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.28 r_work: 0.3049 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14313 Z= 0.152 Angle : 0.529 11.619 19446 Z= 0.278 Chirality : 0.041 0.179 2163 Planarity : 0.004 0.045 2527 Dihedral : 5.949 80.856 1959 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 3.20 % Allowed : 11.24 % Favored : 85.56 % 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: 1.02 (0.20), residues: 1758 helix: 1.58 (0.17), residues: 931 sheet: 0.03 (0.31), residues: 287 loop : -0.45 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 204 TYR 0.016 0.001 TYR B 287 PHE 0.014 0.002 PHE A 181 TRP 0.018 0.001 TRP A 473 HIS 0.006 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00350 (14313) covalent geometry : angle 0.52871 (19446) hydrogen bonds : bond 0.03964 ( 774) hydrogen bonds : angle 4.78057 ( 2200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7870 (mp0) REVERT: A 89 MET cc_start: 0.8129 (mtm) cc_final: 0.7908 (mtm) REVERT: A 187 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8842 (ptm-80) REVERT: A 610 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8738 (ttmm) REVERT: B 14 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7649 (p) REVERT: B 89 MET cc_start: 0.8176 (mtm) cc_final: 0.7896 (mtm) REVERT: B 155 MET cc_start: 0.8508 (ttp) cc_final: 0.8144 (ttt) REVERT: B 248 ASN cc_start: 0.8448 (t0) cc_final: 0.8197 (t0) REVERT: B 610 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8664 (ttmm) REVERT: C 23 VAL cc_start: 0.8666 (t) cc_final: 0.8463 (p) REVERT: C 45 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8207 (mmpt) REVERT: C 71 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8194 (tp-100) REVERT: C 75 GLU cc_start: 0.9082 (pt0) cc_final: 0.8651 (pt0) REVERT: D 21 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7104 (mm-40) REVERT: D 24 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8136 (ptpp) REVERT: D 25 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7815 (mm-30) outliers start: 47 outliers final: 14 residues processed: 175 average time/residue: 0.5032 time to fit residues: 97.7099 Evaluate side-chains 146 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 170 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 197 GLN D 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079636 restraints weight = 35631.919| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.14 r_work: 0.3075 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14313 Z= 0.127 Angle : 0.513 10.037 19446 Z= 0.267 Chirality : 0.041 0.220 2163 Planarity : 0.003 0.042 2527 Dihedral : 5.871 78.443 1959 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 3.07 % Allowed : 11.99 % Favored : 84.95 % 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: 1.13 (0.20), residues: 1758 helix: 1.68 (0.17), residues: 925 sheet: 0.30 (0.32), residues: 265 loop : -0.50 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 204 TYR 0.027 0.001 TYR B 287 PHE 0.015 0.001 PHE C 29 TRP 0.018 0.001 TRP A 473 HIS 0.006 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00287 (14313) covalent geometry : angle 0.51263 (19446) hydrogen bonds : bond 0.03639 ( 774) hydrogen bonds : angle 4.65553 ( 2200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7866 (mp0) REVERT: A 197 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: A 610 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8722 (ttmm) REVERT: A 716 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8414 (mppt) REVERT: B 14 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7669 (p) REVERT: B 89 MET cc_start: 0.8164 (mtm) cc_final: 0.7909 (mtm) REVERT: B 155 MET cc_start: 0.8513 (ttp) cc_final: 0.8160 (ttt) REVERT: B 204 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.8019 (ptp-110) REVERT: B 248 ASN cc_start: 0.8450 (t0) cc_final: 0.8065 (t0) REVERT: B 322 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8561 (p) REVERT: C 45 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8376 (mmtp) REVERT: C 71 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8228 (tp-100) REVERT: C 75 GLU cc_start: 0.9092 (pt0) cc_final: 0.8687 (pt0) REVERT: D 21 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7228 (mm110) REVERT: D 24 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8238 (ptpp) REVERT: D 45 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8535 (mmmt) outliers start: 45 outliers final: 17 residues processed: 165 average time/residue: 0.5394 time to fit residues: 98.2668 Evaluate side-chains 146 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 123 ASN B 159 ASN B 197 GLN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079935 restraints weight = 52016.165| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.77 r_work: 0.3050 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14313 Z= 0.124 Angle : 0.501 9.968 19446 Z= 0.261 Chirality : 0.040 0.197 2163 Planarity : 0.003 0.047 2527 Dihedral : 5.822 77.714 1959 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 2.93 % Allowed : 12.53 % Favored : 84.54 % 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: 1.16 (0.20), residues: 1758 helix: 1.70 (0.17), residues: 926 sheet: 0.35 (0.32), residues: 263 loop : -0.52 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 204 TYR 0.029 0.001 TYR B 287 PHE 0.020 0.001 PHE C 29 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00281 (14313) covalent geometry : angle 0.50127 (19446) hydrogen bonds : bond 0.03552 ( 774) hydrogen bonds : angle 4.59447 ( 2200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.518 Fit side-chains REVERT: A 40 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7934 (mp0) REVERT: A 197 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8804 (mt0) REVERT: A 716 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8372 (mppt) REVERT: B 14 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7725 (p) REVERT: B 89 MET cc_start: 0.8201 (mtm) cc_final: 0.7989 (mtm) REVERT: B 155 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8230 (ttt) REVERT: B 204 ARG cc_start: 0.8350 (ptp-110) cc_final: 0.8043 (ptp-110) REVERT: B 248 ASN cc_start: 0.8500 (t0) cc_final: 0.8069 (t0) REVERT: B 322 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 775 GLU cc_start: 0.8252 (mp0) cc_final: 0.7948 (mp0) REVERT: C 21 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7563 (mm-40) REVERT: C 71 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8216 (tp-100) REVERT: C 75 GLU cc_start: 0.9065 (pt0) cc_final: 0.8666 (pt0) REVERT: D 24 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8215 (ptpp) REVERT: D 25 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7674 (mm-30) outliers start: 43 outliers final: 16 residues processed: 161 average time/residue: 0.5339 time to fit residues: 95.0646 Evaluate side-chains 147 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 197 GLN D 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081139 restraints weight = 44232.191| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.48 r_work: 0.3069 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14313 Z= 0.118 Angle : 0.505 9.626 19446 Z= 0.260 Chirality : 0.040 0.197 2163 Planarity : 0.003 0.053 2527 Dihedral : 5.783 76.578 1959 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 13.22 % Favored : 84.33 % 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: 1.20 (0.21), residues: 1758 helix: 1.75 (0.18), residues: 925 sheet: 0.41 (0.33), residues: 261 loop : -0.54 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 204 TYR 0.034 0.001 TYR B 287 PHE 0.018 0.001 PHE D 29 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00268 (14313) covalent geometry : angle 0.50462 (19446) hydrogen bonds : bond 0.03454 ( 774) hydrogen bonds : angle 4.54244 ( 2200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.525 Fit side-chains REVERT: A 40 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7923 (mp0) REVERT: A 716 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8387 (mppt) REVERT: B 14 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7729 (p) REVERT: B 155 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8188 (ttt) REVERT: B 204 ARG cc_start: 0.8380 (ptp-110) cc_final: 0.8119 (ptp-110) REVERT: B 248 ASN cc_start: 0.8547 (t0) cc_final: 0.8107 (t0) REVERT: B 322 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 775 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7904 (mp0) REVERT: C 71 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8106 (tp-100) REVERT: C 75 GLU cc_start: 0.9075 (pt0) cc_final: 0.8706 (pt0) REVERT: D 21 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7229 (mm-40) REVERT: D 24 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8262 (ptpp) outliers start: 36 outliers final: 18 residues processed: 153 average time/residue: 0.5136 time to fit residues: 87.3555 Evaluate side-chains 146 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 197 GLN D 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079434 restraints weight = 43961.608| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.47 r_work: 0.3051 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14313 Z= 0.146 Angle : 0.524 10.478 19446 Z= 0.270 Chirality : 0.041 0.201 2163 Planarity : 0.004 0.050 2527 Dihedral : 5.826 80.004 1959 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 13.49 % Favored : 84.06 % 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: 1.15 (0.20), residues: 1758 helix: 1.69 (0.17), residues: 926 sheet: 0.38 (0.32), residues: 264 loop : -0.54 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 204 TYR 0.036 0.001 TYR B 287 PHE 0.021 0.001 PHE C 29 TRP 0.015 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00339 (14313) covalent geometry : angle 0.52430 (19446) hydrogen bonds : bond 0.03651 ( 774) hydrogen bonds : angle 4.57186 ( 2200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.495 Fit side-chains REVERT: A 40 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7962 (mp0) REVERT: A 716 LYS cc_start: 0.8612 (mmmm) cc_final: 0.8387 (mppt) REVERT: B 14 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 155 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8219 (ttt) REVERT: B 248 ASN cc_start: 0.8559 (t0) cc_final: 0.8097 (t0) REVERT: B 322 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 775 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7948 (mp0) REVERT: C 45 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8495 (mmmt) REVERT: C 71 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8122 (tp-100) REVERT: C 75 GLU cc_start: 0.9094 (pt0) cc_final: 0.8704 (pt0) REVERT: D 24 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8150 (ptpp) REVERT: D 25 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7910 (mm-30) REVERT: D 45 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8719 (mmmt) outliers start: 36 outliers final: 18 residues processed: 155 average time/residue: 0.5343 time to fit residues: 91.8527 Evaluate side-chains 149 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 157 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 123 ASN B 197 GLN D 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080513 restraints weight = 52077.832| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.92 r_work: 0.3056 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14313 Z= 0.109 Angle : 0.539 16.405 19446 Z= 0.271 Chirality : 0.040 0.205 2163 Planarity : 0.004 0.052 2527 Dihedral : 5.753 74.717 1959 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 1.91 % Allowed : 13.96 % Favored : 84.13 % 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: 1.26 (0.21), residues: 1758 helix: 1.76 (0.18), residues: 925 sheet: 0.53 (0.33), residues: 262 loop : -0.50 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 204 TYR 0.037 0.001 TYR B 287 PHE 0.018 0.001 PHE C 29 TRP 0.017 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00245 (14313) covalent geometry : angle 0.53934 (19446) hydrogen bonds : bond 0.03372 ( 774) hydrogen bonds : angle 4.49502 ( 2200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7909 (mp0) REVERT: A 579 LYS cc_start: 0.8372 (tppt) cc_final: 0.8168 (tppt) REVERT: A 716 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8330 (mppt) REVERT: B 155 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8054 (ttt) REVERT: B 248 ASN cc_start: 0.8542 (t0) cc_final: 0.8079 (t0) REVERT: B 281 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8661 (mm) REVERT: B 322 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8595 (p) REVERT: B 597 MET cc_start: 0.8401 (tpp) cc_final: 0.8168 (tpp) REVERT: C 71 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8161 (tp-100) REVERT: C 75 GLU cc_start: 0.9104 (pt0) cc_final: 0.8753 (pt0) REVERT: D 24 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8181 (ptpp) REVERT: D 25 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7855 (mm-30) REVERT: D 74 VAL cc_start: 0.8569 (p) cc_final: 0.8260 (m) outliers start: 28 outliers final: 13 residues processed: 154 average time/residue: 0.5008 time to fit residues: 85.9160 Evaluate side-chains 141 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 159 ASN B 197 GLN B 305 HIS D 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079009 restraints weight = 50548.873| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.74 r_work: 0.3051 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14313 Z= 0.133 Angle : 0.551 11.935 19446 Z= 0.280 Chirality : 0.041 0.207 2163 Planarity : 0.004 0.055 2527 Dihedral : 5.787 77.415 1959 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.81 % Rotamer: Outliers : 1.57 % Allowed : 14.71 % Favored : 83.72 % 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: 1.24 (0.21), residues: 1758 helix: 1.72 (0.17), residues: 927 sheet: 0.53 (0.33), residues: 262 loop : -0.48 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 204 TYR 0.039 0.001 TYR B 287 PHE 0.016 0.001 PHE C 29 TRP 0.015 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00308 (14313) covalent geometry : angle 0.55145 (19446) hydrogen bonds : bond 0.03527 ( 774) hydrogen bonds : angle 4.53040 ( 2200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7958 (mp0) REVERT: A 103 GLU cc_start: 0.7978 (pp20) cc_final: 0.7584 (pm20) REVERT: A 579 LYS cc_start: 0.8335 (tppt) cc_final: 0.8089 (tppt) REVERT: A 716 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8226 (mmmm) REVERT: B 14 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 40 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: B 155 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8117 (ttt) REVERT: B 248 ASN cc_start: 0.8579 (t0) cc_final: 0.8119 (t0) REVERT: B 281 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 322 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 597 MET cc_start: 0.8448 (tpp) cc_final: 0.8204 (tpp) REVERT: C 71 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8150 (tp-100) REVERT: C 75 GLU cc_start: 0.9100 (pt0) cc_final: 0.8733 (pt0) REVERT: D 74 VAL cc_start: 0.8619 (p) cc_final: 0.8309 (m) outliers start: 23 outliers final: 15 residues processed: 145 average time/residue: 0.5394 time to fit residues: 86.8754 Evaluate side-chains 141 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 87 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 17 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 123 ASN B 339 HIS B 636 GLN D 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081592 restraints weight = 41766.269| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.54 r_work: 0.3090 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14313 Z= 0.104 Angle : 0.543 13.407 19446 Z= 0.272 Chirality : 0.040 0.213 2163 Planarity : 0.004 0.058 2527 Dihedral : 5.610 72.621 1955 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 14.78 % Favored : 83.72 % 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: 1.28 (0.21), residues: 1758 helix: 1.71 (0.17), residues: 932 sheet: 0.64 (0.33), residues: 257 loop : -0.44 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 204 TYR 0.037 0.001 TYR B 287 PHE 0.012 0.001 PHE A 181 TRP 0.018 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00233 (14313) covalent geometry : angle 0.54319 (19446) hydrogen bonds : bond 0.03289 ( 774) hydrogen bonds : angle 4.48480 ( 2200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7899 (mp0) REVERT: A 103 GLU cc_start: 0.7987 (pp20) cc_final: 0.7592 (pm20) REVERT: A 579 LYS cc_start: 0.8342 (tppt) cc_final: 0.8099 (tppt) REVERT: A 716 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8143 (mmmm) REVERT: B 14 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 40 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 155 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7993 (ttt) REVERT: B 241 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8587 (mt-10) REVERT: B 248 ASN cc_start: 0.8576 (t0) cc_final: 0.8124 (t0) REVERT: B 281 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8628 (mm) REVERT: B 597 MET cc_start: 0.8386 (tpp) cc_final: 0.8158 (tpp) REVERT: B 705 ARG cc_start: 0.8462 (mtm110) cc_final: 0.8259 (mtm110) REVERT: C 25 GLU cc_start: 0.8045 (mp0) cc_final: 0.7771 (mp0) REVERT: C 71 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8135 (tp-100) REVERT: C 75 GLU cc_start: 0.9094 (pt0) cc_final: 0.8744 (pt0) outliers start: 22 outliers final: 15 residues processed: 149 average time/residue: 0.4960 time to fit residues: 82.8070 Evaluate side-chains 145 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 69 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 197 GLN D 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080074 restraints weight = 38616.627| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.30 r_work: 0.3069 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14313 Z= 0.139 Angle : 0.565 15.778 19446 Z= 0.285 Chirality : 0.041 0.211 2163 Planarity : 0.004 0.057 2527 Dihedral : 5.677 77.255 1955 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 15.05 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.25 (0.21), residues: 1758 helix: 1.72 (0.17), residues: 926 sheet: 0.51 (0.33), residues: 262 loop : -0.43 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 204 TYR 0.037 0.001 TYR B 287 PHE 0.017 0.001 PHE C 29 TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00324 (14313) covalent geometry : angle 0.56487 (19446) hydrogen bonds : bond 0.03540 ( 774) hydrogen bonds : angle 4.52848 ( 2200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4403.66 seconds wall clock time: 76 minutes 2.13 seconds (4562.13 seconds total)