Starting phenix.real_space_refine on Fri Aug 7 17:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1b_40958/08_2026/8t1b_40958_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1b_40958/08_2026/8t1b_40958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t1b_40958/08_2026/8t1b_40958_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1b_40958/08_2026/8t1b_40958_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t1b_40958/08_2026/8t1b_40958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1b_40958/08_2026/8t1b_40958.map" } resolution = 3.0 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= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 108 5.16 5 Na 4 4.78 5 C 15404 2.51 5 N 3472 2.21 5 O 4156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23180 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5176 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 26, 'TRANS': 617} Chain breaks: 1 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5176 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 26, 'TRANS': 617} Chain breaks: 1 Chain: "C" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5176 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 26, 'TRANS': 617} Chain breaks: 1 Chain: "D" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5176 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 26, 'TRANS': 617} Chain breaks: 1 Chain: "A" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 660 Unusual residues: {' NA': 4, '9ZR': 11, 'YJ0': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'9ZR:plan-4': 3, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 544 Unusual residues: {'9ZR': 9, 'YJ0': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'9ZR:plan-4': 3, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 600 Unusual residues: {'9ZR': 10, 'YJ0': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'9ZR:plan-4': 3, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 600 Unusual residues: {'9ZR': 10, 'YJ0': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'9ZR:plan-4': 3, '9ZR:plan-1': 1, '9ZR:plan-2': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 5.31, per 1000 atoms: 0.23 Number of scatterers: 23180 At special positions: 0 Unit cell: (133.63, 133.63, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 36 15.00 Na 4 11.00 O 4156 8.00 N 3472 7.00 C 15404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 639 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.03 Simple disulfide: pdb=" SG CYS D 639 " - pdb=" SG CYS D 660 " distance=2.03 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4856 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 58.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.676A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.943A pdb=" N THR A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.572A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.556A pdb=" N LEU A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.675A pdb=" N GLU A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.928A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.697A pdb=" N VAL A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.788A pdb=" N THR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.596A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.839A pdb=" N VAL A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 removed outlier: 3.544A pdb=" N ASN A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.733A pdb=" N LEU A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 3.609A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.773A pdb=" N ARG A 594 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.615A pdb=" N ILE A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.641A pdb=" N LEU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.660A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.524A pdb=" N ILE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.425A pdb=" N GLU A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 754 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.944A pdb=" N THR B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.571A pdb=" N LEU B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.556A pdb=" N LEU B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.675A pdb=" N GLU B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.928A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 297 through 304 removed outlier: 3.695A pdb=" N VAL B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.787A pdb=" N THR B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.597A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 466 through 491 removed outlier: 3.839A pdb=" N VAL B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 534 removed outlier: 3.544A pdb=" N ASN B 528 " --> pdb=" O PHE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 570 removed outlier: 3.733A pdb=" N LEU B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 588 removed outlier: 3.609A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.774A pdb=" N ARG B 594 " --> pdb=" O TYR B 591 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY B 595 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.615A pdb=" N ILE B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.641A pdb=" N LEU B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.660A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 723 removed outlier: 3.524A pdb=" N ILE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.424A pdb=" N GLU B 728 " --> pdb=" O GLN B 724 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.676A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 156 " --> pdb=" O PRO C 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.944A pdb=" N THR C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.572A pdb=" N LEU C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.556A pdb=" N LEU C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 215 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.674A pdb=" N GLU C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.927A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 297 through 304 removed outlier: 3.697A pdb=" N VAL C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 356 removed outlier: 3.788A pdb=" N THR C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.597A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.839A pdb=" N VAL C 476 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 488 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 534 removed outlier: 3.545A pdb=" N ASN C 528 " --> pdb=" O PHE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 570 removed outlier: 3.733A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 removed outlier: 3.609A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.774A pdb=" N ARG C 594 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.614A pdb=" N ILE C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 634 Processing helix chain 'C' and resid 664 through 679 removed outlier: 3.641A pdb=" N LEU C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 707 removed outlier: 3.660A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.524A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 747 removed outlier: 4.423A pdb=" N GLU C 728 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 734 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 754 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.676A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 156 " --> pdb=" O PRO D 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 159 " --> pdb=" O PHE D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.945A pdb=" N THR D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.572A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 removed outlier: 3.556A pdb=" N LEU D 214 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.675A pdb=" N GLU D 247 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.927A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 297 through 304 removed outlier: 3.696A pdb=" N VAL D 301 " --> pdb=" O GLN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.788A pdb=" N THR D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 354 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.596A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.839A pdb=" N VAL D 476 " --> pdb=" O TYR D 472 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 488 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 534 removed outlier: 3.544A pdb=" N ASN D 528 " --> pdb=" O PHE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 570 removed outlier: 3.733A pdb=" N LEU D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 588 removed outlier: 3.609A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.775A pdb=" N ARG D 594 " --> pdb=" O TYR D 591 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 595 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.616A pdb=" N ILE D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 634 Processing helix chain 'D' and resid 664 through 679 removed outlier: 3.641A pdb=" N LEU D 671 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 707 removed outlier: 3.660A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 723 removed outlier: 3.524A pdb=" N ILE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 718 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 747 removed outlier: 4.424A pdb=" N GLU D 728 " --> pdb=" O GLN D 724 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 734 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 735 " --> pdb=" O HIS D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 754 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.891A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY A 765 " --> pdb=" O ASP A 773 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG A 775 " --> pdb=" O THR A 763 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR A 763 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS A 777 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N MET A 761 " --> pdb=" O CYS A 777 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.890A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 765 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG B 775 " --> pdb=" O THR B 763 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR B 763 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 777 " --> pdb=" O MET B 761 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N MET B 761 " --> pdb=" O CYS B 777 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.890A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY C 765 " --> pdb=" O ASP C 773 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG C 775 " --> pdb=" O THR C 763 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR C 763 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS C 777 " --> pdb=" O MET C 761 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N MET C 761 " --> pdb=" O CYS C 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.890A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY D 765 " --> pdb=" O ASP D 773 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG D 775 " --> pdb=" O THR D 763 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR D 763 " --> pdb=" O ARG D 775 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS D 777 " --> pdb=" O MET D 761 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N MET D 761 " --> pdb=" O CYS D 777 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3703 1.32 - 1.45: 5915 1.45 - 1.57: 13722 1.57 - 1.69: 84 1.69 - 1.82: 176 Bond restraints: 23600 Sorted by residual: bond pdb=" O32 9ZR B1204 " pdb=" P29 9ZR B1204 " ideal model delta sigma weight residual 1.661 1.592 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O32 9ZR D1205 " pdb=" P29 9ZR D1205 " ideal model delta sigma weight residual 1.661 1.592 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O32 9ZR A1203 " pdb=" P29 9ZR A1203 " ideal model delta sigma weight residual 1.661 1.592 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O32 9ZR A1206 " pdb=" P29 9ZR A1206 " ideal model delta sigma weight residual 1.661 1.592 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O32 9ZR C1205 " pdb=" P29 9ZR C1205 " ideal model delta sigma weight residual 1.661 1.592 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 23595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 29721 2.35 - 4.70: 1517 4.70 - 7.05: 326 7.05 - 9.40: 104 9.40 - 11.75: 28 Bond angle restraints: 31696 Sorted by residual: angle pdb=" CG1 VAL A 764 " pdb=" CB VAL A 764 " pdb=" CG2 VAL A 764 " ideal model delta sigma weight residual 110.80 122.45 -11.65 2.20e+00 2.07e-01 2.80e+01 angle pdb=" CG1 VAL C 764 " pdb=" CB VAL C 764 " pdb=" CG2 VAL C 764 " ideal model delta sigma weight residual 110.80 122.45 -11.65 2.20e+00 2.07e-01 2.80e+01 angle pdb=" CG1 VAL D 764 " pdb=" CB VAL D 764 " pdb=" CG2 VAL D 764 " ideal model delta sigma weight residual 110.80 122.43 -11.63 2.20e+00 2.07e-01 2.80e+01 angle pdb=" CG1 VAL B 764 " pdb=" CB VAL B 764 " pdb=" CG2 VAL B 764 " ideal model delta sigma weight residual 110.80 122.40 -11.60 2.20e+00 2.07e-01 2.78e+01 angle pdb=" CG1 VAL D 540 " pdb=" CB VAL D 540 " pdb=" CG2 VAL D 540 " ideal model delta sigma weight residual 110.80 122.20 -11.40 2.20e+00 2.07e-01 2.69e+01 ... (remaining 31691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 14610 35.86 - 71.72: 638 71.72 - 107.58: 299 107.58 - 143.45: 72 143.45 - 179.31: 57 Dihedral angle restraints: 15676 sinusoidal: 8136 harmonic: 7540 Sorted by residual: dihedral pdb=" CA GLU D 453 " pdb=" C GLU D 453 " pdb=" N PRO D 454 " pdb=" CA PRO D 454 " ideal model delta harmonic sigma weight residual -180.00 -129.26 -50.74 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA GLU A 453 " pdb=" C GLU A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual 180.00 -129.28 -50.72 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA GLU B 453 " pdb=" C GLU B 453 " pdb=" N PRO B 454 " pdb=" CA PRO B 454 " ideal model delta harmonic sigma weight residual -180.00 -129.29 -50.71 0 5.00e+00 4.00e-02 1.03e+02 ... (remaining 15673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 3404 0.346 - 0.691: 40 0.691 - 1.037: 0 1.037 - 1.382: 0 1.382 - 1.728: 16 Chirality restraints: 3460 Sorted by residual: chirality pdb=" CB VAL A 764 " pdb=" CA VAL A 764 " pdb=" CG1 VAL A 764 " pdb=" CG2 VAL A 764 " both_signs ideal model delta sigma weight residual False -2.63 -0.90 -1.73 2.00e-01 2.50e+01 7.46e+01 chirality pdb=" CB VAL D 764 " pdb=" CA VAL D 764 " pdb=" CG1 VAL D 764 " pdb=" CG2 VAL D 764 " both_signs ideal model delta sigma weight residual False -2.63 -0.90 -1.73 2.00e-01 2.50e+01 7.46e+01 chirality pdb=" CB VAL B 764 " pdb=" CA VAL B 764 " pdb=" CG1 VAL B 764 " pdb=" CG2 VAL B 764 " both_signs ideal model delta sigma weight residual False -2.63 -0.90 -1.73 2.00e-01 2.50e+01 7.45e+01 ... (remaining 3457 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 C1212 " -0.219 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" C18 YJ0 C1212 " 0.270 2.00e-02 2.50e+03 pdb=" C19 YJ0 C1212 " 0.124 2.00e-02 2.50e+03 pdb=" C20 YJ0 C1212 " 0.008 2.00e-02 2.50e+03 pdb=" C24 YJ0 C1212 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 B1211 " 0.219 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" C18 YJ0 B1211 " -0.269 2.00e-02 2.50e+03 pdb=" C19 YJ0 B1211 " -0.124 2.00e-02 2.50e+03 pdb=" C20 YJ0 B1211 " -0.008 2.00e-02 2.50e+03 pdb=" C24 YJ0 B1211 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 A1210 " 0.219 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" C18 YJ0 A1210 " -0.270 2.00e-02 2.50e+03 pdb=" C19 YJ0 A1210 " -0.123 2.00e-02 2.50e+03 pdb=" C20 YJ0 A1210 " -0.008 2.00e-02 2.50e+03 pdb=" C24 YJ0 A1210 " 0.181 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 361 2.60 - 3.17: 20306 3.17 - 3.75: 34295 3.75 - 4.32: 52267 4.32 - 4.90: 83498 Nonbonded interactions: 190727 Sorted by model distance: nonbonded pdb=" OH TYR C 283 " pdb=" OD2 ASP C 318 " model vdw 2.024 3.040 nonbonded pdb=" OH TYR A 283 " pdb=" OD2 ASP A 318 " model vdw 2.025 3.040 nonbonded pdb=" OH TYR B 283 " pdb=" OD2 ASP B 318 " model vdw 2.025 3.040 nonbonded pdb=" OH TYR D 283 " pdb=" OD2 ASP D 318 " model vdw 2.025 3.040 nonbonded pdb=" O TYR A 702 " pdb=" OG1 THR A 706 " model vdw 2.072 3.040 ... (remaining 190722 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 148 through 1201 or resid 1204 through 1205 or (resid 1206 \ through 1207 and (name C44 or name C45 or name C46 or name C47 or name C48 or n \ ame C49 or name C50 or name C51 or name C52 or name C53 or name C54 or name C55 \ or name C56)) or resid 1208 through 1209)) selection = (chain 'B' and (resid 148 through 1201 or (resid 1204 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C25 or name C26 or name C27 or name C33 or name C34 or n \ ame C36 or name C37 or name C38 or name C40 or name C42 or name C43 or name C44 \ or name C45 or name C46 or name C47 or name C48 or name C49 or name C50 or name \ C51 or name C52 or name C53 or name C54 or name C55 or name C56 or name N35 or n \ ame O23 or name O24 or name O28 or name O30 or name O31 or name O32 or name O39 \ or name O41 or name P29)) or (resid 1205 through 1207 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or resid 1208 or (resid 12 \ 09 and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C25 \ or name C26 or name C27 or name C33 or name C34 or name C36 or name C37 or name \ C38 or name C40 or name C42 or name C43 or name C44 or name C45 or name C46 or \ name C47 or name C48 or name C49 or name C50 or name C51 or name C52 or name C53 \ or name C54 or name C55 or name C56 or name N35 or name O23 or name O24 or name \ O28 or name O30 or name O31 or name O32 or name O39 or name O41 or name P29)))) \ selection = (chain 'C' and (resid 148 through 1201 or (resid 1204 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C25 or name C26 or name C27 or name C33 or name C34 or n \ ame C36 or name C37 or name C38 or name C40 or name C42 or name C43 or name C44 \ or name C45 or name C46 or name C47 or name C48 or name C49 or name C50 or name \ C51 or name C52 or name C53 or name C54 or name C55 or name C56 or name N35 or n \ ame O23 or name O24 or name O28 or name O30 or name O31 or name O32 or name O39 \ or name O41 or name P29)) or (resid 1205 through 1207 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or resid 1208 or (resid 12 \ 09 and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C25 \ or name C26 or name C27 or name C33 or name C34 or name C36 or name C37 or name \ C38 or name C40 or name C42 or name C43 or name C44 or name C45 or name C46 or \ name C47 or name C48 or name C49 or name C50 or name C51 or name C52 or name C53 \ or name C54 or name C55 or name C56 or name N35 or name O23 or name O24 or name \ O28 or name O30 or name O31 or name O32 or name O39 or name O41 or name P29)))) \ selection = (chain 'D' and (resid 148 through 1201 or (resid 1204 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C25 or name C26 or name C27 or name C33 or name C34 or n \ ame C36 or name C37 or name C38 or name C40 or name C42 or name C43 or name C44 \ or name C45 or name C46 or name C47 or name C48 or name C49 or name C50 or name \ C51 or name C52 or name C53 or name C54 or name C55 or name C56 or name N35 or n \ ame O23 or name O24 or name O28 or name O30 or name O31 or name O32 or name O39 \ or name O41 or name P29)) or (resid 1205 through 1207 and (name C44 or name C45 \ or name C46 or name C47 or name C48 or name C49 or name C50 or name C51 or name \ C52 or name C53 or name C54 or name C55 or name C56)) or resid 1208 or (resid 12 \ 09 and (name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C25 \ or name C26 or name C27 or name C33 or name C34 or name C36 or name C37 or name \ C38 or name C40 or name C42 or name C43 or name C44 or name C45 or name C46 or \ name C47 or name C48 or name C49 or name C50 or name C51 or name C52 or name C53 \ or name C54 or name C55 or name C56 or name N35 or name O23 or name O24 or name \ O28 or name O30 or name O31 or name O32 or name O39 or name O41 or name P29)))) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.240 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.010 0.069 23604 Z= 0.439 Angle : 1.315 11.754 31704 Z= 0.635 Chirality : 0.136 1.728 3460 Planarity : 0.010 0.184 3756 Dihedral : 26.617 179.306 10808 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.45 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.16 % 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: -5.72 (0.12), residues: 2560 helix: -3.70 (0.09), residues: 1452 sheet: -2.36 (0.62), residues: 76 loop : -3.89 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 594 TYR 0.021 0.002 TYR C 602 PHE 0.024 0.003 PHE D 669 TRP 0.017 0.002 TRP A 733 HIS 0.003 0.001 HIS D 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00999 / 0.44 (23600) covalent geometry : angle 1.31513 / 0.63 (31696) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 1.49207 / 0.81 ( 8) hydrogen bonds : bond 0.28160 / 18.70 ( 955) hydrogen bonds : angle 10.46984 / 7.29 ( 2805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.7211 (m-80) cc_final: 0.6176 (m-80) REVERT: A 315 ARG cc_start: 0.7241 (mpt180) cc_final: 0.7013 (mpp80) REVERT: A 615 PHE cc_start: 0.7194 (m-10) cc_final: 0.6864 (t80) REVERT: B 192 LYS cc_start: 0.6397 (ttmm) cc_final: 0.6113 (tttt) REVERT: B 201 ASN cc_start: 0.7244 (m-40) cc_final: 0.6989 (m-40) REVERT: B 315 ARG cc_start: 0.7170 (mpt180) cc_final: 0.6494 (mpp80) REVERT: B 391 ARG cc_start: 0.7322 (ptt180) cc_final: 0.6867 (ptp-170) REVERT: C 192 LYS cc_start: 0.6423 (ttmm) cc_final: 0.6095 (tttt) REVERT: C 197 LYS cc_start: 0.7602 (tppp) cc_final: 0.7169 (tppt) REVERT: C 201 ASN cc_start: 0.7170 (m-40) cc_final: 0.6871 (m110) REVERT: C 315 ARG cc_start: 0.7162 (mpt180) cc_final: 0.6519 (mpp80) REVERT: C 391 ARG cc_start: 0.7261 (ptt180) cc_final: 0.6787 (ptp-170) REVERT: C 799 PRO cc_start: 0.7532 (Cg_exo) cc_final: 0.7230 (Cg_endo) REVERT: D 192 LYS cc_start: 0.6414 (ttmm) cc_final: 0.6193 (tttt) REVERT: D 201 ASN cc_start: 0.7118 (m-40) cc_final: 0.6893 (m110) REVERT: D 236 TYR cc_start: 0.6994 (m-80) cc_final: 0.6664 (m-80) REVERT: D 315 ARG cc_start: 0.7237 (mpt180) cc_final: 0.6551 (mpp80) REVERT: D 799 PRO cc_start: 0.7414 (Cg_exo) cc_final: 0.7148 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.5116 time to fit residues: 281.3197 Evaluate side-chains 261 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 176 HIS A 201 ASN A 207 ASN A 228 ASN A 260 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 326 HIS A 588 ASN A 784 ASN B 176 HIS B 201 ASN B 207 ASN B 228 ASN B 243 HIS B 260 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 528 ASN B 588 ASN B 784 ASN B 787 HIS C 176 HIS C 201 ASN C 207 ASN C 228 ASN C 243 HIS C 260 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS C 528 ASN C 588 ASN C 784 ASN C 787 HIS D 176 HIS D 201 ASN D 207 ASN D 228 ASN D 243 HIS D 260 GLN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS D 528 ASN D 588 ASN D 784 ASN D 787 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.207345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.169238 restraints weight = 24839.206| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.92 r_work: 0.3680 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23604 Z= 0.162 Angle : 0.794 11.816 31704 Z= 0.381 Chirality : 0.044 0.238 3460 Planarity : 0.006 0.082 3756 Dihedral : 30.290 177.076 5892 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.52 % Favored : 91.05 % Rotamer: Outliers : 2.46 % Allowed : 9.33 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.29 (0.15), residues: 2560 helix: -1.33 (0.12), residues: 1484 sheet: -2.20 (0.61), residues: 76 loop : -3.48 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 779 TYR 0.021 0.001 TYR C 657 PHE 0.021 0.002 PHE B 485 TRP 0.025 0.002 TRP A 733 HIS 0.004 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (23600) covalent geometry : angle 0.79351 / 0.38 (31696) SS BOND : bond 0.00027 / 0.01 ( 4) SS BOND : angle 1.19784 / 0.65 ( 8) hydrogen bonds : bond 0.04223 / 2.80 ( 955) hydrogen bonds : angle 4.81701 / 3.39 ( 2805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6414 (mp0) cc_final: 0.6045 (mp0) REVERT: A 236 TYR cc_start: 0.7161 (m-80) cc_final: 0.6515 (m-80) REVERT: A 315 ARG cc_start: 0.7585 (mpt180) cc_final: 0.6946 (mpp80) REVERT: B 315 ARG cc_start: 0.7157 (mpt180) cc_final: 0.6374 (mpp80) REVERT: B 350 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6609 (tp) REVERT: B 397 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: C 315 ARG cc_start: 0.7203 (mpt180) cc_final: 0.6393 (mpp80) REVERT: C 350 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6593 (tp) REVERT: C 397 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: C 411 TYR cc_start: 0.8376 (t80) cc_final: 0.8150 (t80) REVERT: C 672 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: D 315 ARG cc_start: 0.7170 (mpt180) cc_final: 0.6411 (mpp80) REVERT: D 350 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6602 (tp) REVERT: D 397 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7834 (pm20) outliers start: 56 outliers final: 8 residues processed: 366 average time/residue: 0.4848 time to fit residues: 208.0276 Evaluate side-chains 258 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 771 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 787 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.198409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158386 restraints weight = 25122.358| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.04 r_work: 0.3538 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23604 Z= 0.187 Angle : 0.787 11.579 31704 Z= 0.376 Chirality : 0.044 0.240 3460 Planarity : 0.006 0.088 3756 Dihedral : 28.686 179.568 5892 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.52 % Favored : 91.02 % Rotamer: Outliers : 3.08 % Allowed : 13.34 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.16), residues: 2560 helix: -0.43 (0.13), residues: 1460 sheet: -2.34 (0.64), residues: 76 loop : -3.16 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 315 TYR 0.032 0.002 TYR B 657 PHE 0.023 0.002 PHE C 485 TRP 0.025 0.002 TRP A 733 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (23600) covalent geometry : angle 0.78704 / 0.38 (31696) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.95622 / 0.52 ( 8) hydrogen bonds : bond 0.04240 / 2.82 ( 955) hydrogen bonds : angle 4.56832 / 3.23 ( 2805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6479 (mp0) cc_final: 0.6154 (mp0) REVERT: A 320 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6850 (mtp85) REVERT: A 397 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: A 607 GLN cc_start: 0.8741 (tt0) cc_final: 0.8118 (mp10) REVERT: A 615 PHE cc_start: 0.7664 (m-10) cc_final: 0.6966 (t80) REVERT: B 310 LYS cc_start: 0.8162 (tttt) cc_final: 0.7934 (tttp) REVERT: B 315 ARG cc_start: 0.7432 (mpt180) cc_final: 0.6775 (mtm110) REVERT: B 397 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: B 607 GLN cc_start: 0.8724 (tt0) cc_final: 0.8085 (mp10) REVERT: B 680 MET cc_start: 0.7865 (ptp) cc_final: 0.7636 (ptp) REVERT: C 315 ARG cc_start: 0.7431 (mpt180) cc_final: 0.6835 (mtm110) REVERT: C 607 GLN cc_start: 0.8757 (tt0) cc_final: 0.8061 (mp10) REVERT: C 680 MET cc_start: 0.7881 (ptp) cc_final: 0.7658 (ptp) REVERT: D 315 ARG cc_start: 0.7459 (mpt180) cc_final: 0.6792 (mtm110) REVERT: D 411 TYR cc_start: 0.8480 (t80) cc_final: 0.8250 (t80) REVERT: D 607 GLN cc_start: 0.8756 (tt0) cc_final: 0.8089 (mp10) outliers start: 70 outliers final: 24 residues processed: 366 average time/residue: 0.5502 time to fit residues: 232.7255 Evaluate side-chains 277 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 105 optimal weight: 0.2980 chunk 254 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 242 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS C 787 HIS D 787 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.198820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156950 restraints weight = 25002.194| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.02 r_work: 0.3574 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23604 Z= 0.127 Angle : 0.692 10.068 31704 Z= 0.332 Chirality : 0.041 0.234 3460 Planarity : 0.005 0.076 3756 Dihedral : 27.145 179.930 5892 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.24 % Favored : 91.29 % Rotamer: Outliers : 2.68 % Allowed : 14.83 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.04 % 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: -1.46 (0.17), residues: 2560 helix: 0.26 (0.13), residues: 1468 sheet: -2.27 (0.66), residues: 76 loop : -2.77 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.016 0.001 TYR A 657 PHE 0.014 0.001 PHE B 341 TRP 0.019 0.002 TRP A 733 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (23600) covalent geometry : angle 0.69230 / 0.33 (31696) SS BOND : bond 0.00126 / 0.06 ( 4) SS BOND : angle 0.91932 / 0.49 ( 8) hydrogen bonds : bond 0.03393 / 2.25 ( 955) hydrogen bonds : angle 4.18803 / 2.95 ( 2805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 293 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6400 (mp0) cc_final: 0.6004 (mp0) REVERT: A 664 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5626 (pm20) REVERT: A 766 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7760 (tptm) REVERT: B 350 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6439 (tp) REVERT: B 353 CYS cc_start: 0.5518 (OUTLIER) cc_final: 0.5170 (p) REVERT: C 350 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6384 (tp) REVERT: C 353 CYS cc_start: 0.5508 (OUTLIER) cc_final: 0.5147 (p) REVERT: C 397 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: C 607 GLN cc_start: 0.8692 (tt0) cc_final: 0.8110 (mp10) REVERT: D 193 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.6161 (p) REVERT: D 350 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6419 (tp) REVERT: D 353 CYS cc_start: 0.5518 (OUTLIER) cc_final: 0.5149 (p) REVERT: D 397 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: D 411 TYR cc_start: 0.8412 (t80) cc_final: 0.8208 (t80) outliers start: 61 outliers final: 16 residues processed: 335 average time/residue: 0.5104 time to fit residues: 199.2456 Evaluate side-chains 268 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 613 ASP Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 528 ASN B 787 HIS C 787 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.196631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155272 restraints weight = 24743.941| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.81 r_work: 0.3486 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23604 Z= 0.162 Angle : 0.743 12.034 31704 Z= 0.357 Chirality : 0.043 0.238 3460 Planarity : 0.005 0.087 3756 Dihedral : 26.375 178.524 5892 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.91 % Favored : 90.62 % Rotamer: Outliers : 2.86 % Allowed : 15.10 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.04 % 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 (0.17), residues: 2560 helix: 0.42 (0.13), residues: 1456 sheet: -2.46 (0.67), residues: 68 loop : -2.66 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 779 TYR 0.022 0.002 TYR C 657 PHE 0.015 0.001 PHE B 485 TRP 0.019 0.002 TRP A 733 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (23600) covalent geometry : angle 0.74262 / 0.36 (31696) SS BOND : bond 0.00110 / 0.05 ( 4) SS BOND : angle 0.87506 / 0.47 ( 8) hydrogen bonds : bond 0.03718 / 2.46 ( 955) hydrogen bonds : angle 4.24341 / 2.98 ( 2805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6136 (mp0) cc_final: 0.5673 (mp0) REVERT: A 411 TYR cc_start: 0.8480 (t80) cc_final: 0.8200 (t80) REVERT: A 607 GLN cc_start: 0.8788 (tt0) cc_final: 0.8176 (mp10) REVERT: A 766 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7671 (tppp) REVERT: B 397 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: B 448 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7863 (pt0) REVERT: B 607 GLN cc_start: 0.8753 (tt0) cc_final: 0.8124 (mp10) REVERT: C 271 ARG cc_start: 0.7453 (tpt-90) cc_final: 0.7243 (tpt170) REVERT: C 397 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: C 607 GLN cc_start: 0.8778 (tt0) cc_final: 0.8146 (mp10) REVERT: C 615 PHE cc_start: 0.7651 (m-10) cc_final: 0.7023 (t80) REVERT: D 193 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.6233 (p) REVERT: D 397 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: D 534 MET cc_start: 0.5800 (tmm) cc_final: 0.5548 (tmm) REVERT: D 607 GLN cc_start: 0.8755 (tt0) cc_final: 0.8142 (mp10) REVERT: D 615 PHE cc_start: 0.7628 (m-10) cc_final: 0.7014 (t80) outliers start: 65 outliers final: 29 residues processed: 318 average time/residue: 0.4883 time to fit residues: 181.1206 Evaluate side-chains 278 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 235 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 791 ASN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS D 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.199788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162087 restraints weight = 25090.504| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.67 r_work: 0.3580 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23604 Z= 0.135 Angle : 0.696 11.809 31704 Z= 0.331 Chirality : 0.041 0.238 3460 Planarity : 0.005 0.079 3756 Dihedral : 25.520 178.250 5892 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.16 % Favored : 91.41 % Rotamer: Outliers : 2.82 % Allowed : 15.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.04 % 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: -0.91 (0.17), residues: 2560 helix: 0.69 (0.14), residues: 1468 sheet: -1.77 (0.68), residues: 76 loop : -2.54 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.017 0.001 TYR D 657 PHE 0.014 0.001 PHE B 341 TRP 0.017 0.002 TRP B 733 HIS 0.008 0.001 HIS B 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (23600) covalent geometry : angle 0.69566 / 0.33 (31696) SS BOND : bond 0.00095 / 0.04 ( 4) SS BOND : angle 0.82957 / 0.45 ( 8) hydrogen bonds : bond 0.03399 / 2.25 ( 955) hydrogen bonds : angle 4.14755 / 2.93 ( 2805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6051 (mp0) cc_final: 0.5616 (mp0) REVERT: A 411 TYR cc_start: 0.8442 (t80) cc_final: 0.8153 (t80) REVERT: A 448 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7684 (pt0) REVERT: A 607 GLN cc_start: 0.8647 (tt0) cc_final: 0.8129 (mp10) REVERT: A 766 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7688 (tppp) REVERT: A 782 GLU cc_start: 0.7752 (tp30) cc_final: 0.7476 (mm-30) REVERT: B 274 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7558 (mm-40) REVERT: B 397 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: B 448 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7749 (pt0) REVERT: B 607 GLN cc_start: 0.8623 (tt0) cc_final: 0.8100 (mp10) REVERT: B 766 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7589 (tppp) REVERT: C 397 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: C 607 GLN cc_start: 0.8642 (tt0) cc_final: 0.8127 (mp10) REVERT: D 193 THR cc_start: 0.6517 (OUTLIER) cc_final: 0.6270 (p) REVERT: D 274 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: D 397 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: D 607 GLN cc_start: 0.8643 (tt0) cc_final: 0.8130 (mp10) REVERT: D 766 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7607 (tppp) REVERT: D 782 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7450 (tm-30) outliers start: 64 outliers final: 23 residues processed: 317 average time/residue: 0.4500 time to fit residues: 167.2732 Evaluate side-chains 289 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 41 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 154 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.197486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150855 restraints weight = 25197.126| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.97 r_work: 0.3543 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23604 Z= 0.128 Angle : 0.685 12.489 31704 Z= 0.327 Chirality : 0.041 0.245 3460 Planarity : 0.005 0.079 3756 Dihedral : 24.796 178.302 5892 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.20 % Favored : 91.41 % Rotamer: Outliers : 2.29 % Allowed : 17.21 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.04 % 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: -0.76 (0.17), residues: 2560 helix: 0.72 (0.14), residues: 1496 sheet: -1.87 (0.65), residues: 68 loop : -2.37 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.016 0.001 TYR D 657 PHE 0.014 0.001 PHE B 341 TRP 0.016 0.002 TRP A 733 HIS 0.006 0.001 HIS B 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (23600) covalent geometry : angle 0.68527 / 0.33 (31696) SS BOND : bond 0.00118 / 0.05 ( 4) SS BOND : angle 0.80972 / 0.44 ( 8) hydrogen bonds : bond 0.03335 / 2.21 ( 955) hydrogen bonds : angle 4.13011 / 2.93 ( 2805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.5870 (mp0) cc_final: 0.5391 (mp0) REVERT: A 310 LYS cc_start: 0.7487 (tttt) cc_final: 0.7267 (tttp) REVERT: A 315 ARG cc_start: 0.7572 (mpt180) cc_final: 0.6930 (mpp80) REVERT: A 411 TYR cc_start: 0.8562 (t80) cc_final: 0.8271 (t80) REVERT: A 448 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7787 (pt0) REVERT: A 607 GLN cc_start: 0.8729 (tt0) cc_final: 0.8092 (mp10) REVERT: A 766 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7539 (tppp) REVERT: A 782 GLU cc_start: 0.7783 (tp30) cc_final: 0.7535 (mm-30) REVERT: B 274 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7545 (mm110) REVERT: B 397 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: B 448 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7859 (pt0) REVERT: B 607 GLN cc_start: 0.8695 (tt0) cc_final: 0.8042 (mp10) REVERT: B 766 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7508 (tppp) REVERT: C 397 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: C 607 GLN cc_start: 0.8716 (tt0) cc_final: 0.8078 (mp10) REVERT: C 766 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7505 (tppp) REVERT: D 193 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6179 (p) REVERT: D 274 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7583 (mm-40) REVERT: D 397 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: D 607 GLN cc_start: 0.8766 (tt0) cc_final: 0.8103 (mp10) REVERT: D 766 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7540 (tppp) outliers start: 52 outliers final: 25 residues processed: 306 average time/residue: 0.4814 time to fit residues: 172.3761 Evaluate side-chains 293 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 146 optimal weight: 0.0030 chunk 139 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 221 optimal weight: 0.0570 chunk 186 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 123 optimal weight: 0.0070 chunk 212 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 401 HIS B 791 ASN C 260 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS C 791 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.203338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.164880 restraints weight = 24891.605| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.69 r_work: 0.3627 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23604 Z= 0.115 Angle : 0.675 12.584 31704 Z= 0.322 Chirality : 0.040 0.247 3460 Planarity : 0.005 0.078 3756 Dihedral : 24.006 179.862 5892 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.36 % Favored : 91.33 % Rotamer: Outliers : 1.94 % Allowed : 18.13 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -0.42 (0.18), residues: 2560 helix: 1.01 (0.14), residues: 1476 sheet: -1.90 (0.52), residues: 104 loop : -2.17 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 746 TYR 0.013 0.001 TYR D 657 PHE 0.013 0.001 PHE B 341 TRP 0.018 0.001 TRP D 737 HIS 0.009 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (23600) covalent geometry : angle 0.67491 / 0.32 (31696) SS BOND : bond 0.00169 / 0.08 ( 4) SS BOND : angle 0.80306 / 0.44 ( 8) hydrogen bonds : bond 0.03143 / 2.09 ( 955) hydrogen bonds : angle 4.01442 / 2.86 ( 2805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.7199 (t80) cc_final: 0.6984 (t80) REVERT: A 315 ARG cc_start: 0.7124 (mpt180) cc_final: 0.6766 (mpp80) REVERT: A 411 TYR cc_start: 0.8464 (t80) cc_final: 0.8152 (t80) REVERT: A 607 GLN cc_start: 0.8609 (tt0) cc_final: 0.8155 (mp10) REVERT: A 664 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: A 766 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7581 (tppp) REVERT: B 274 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7578 (mm-40) REVERT: B 607 GLN cc_start: 0.8623 (tt0) cc_final: 0.8119 (mp10) REVERT: B 766 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7567 (tppp) REVERT: C 607 GLN cc_start: 0.8608 (tt0) cc_final: 0.8139 (mp10) REVERT: C 766 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7567 (tppp) REVERT: D 193 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6196 (p) REVERT: D 274 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7584 (mm110) REVERT: D 607 GLN cc_start: 0.8661 (tt0) cc_final: 0.8148 (mp10) REVERT: D 766 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7586 (tppp) outliers start: 44 outliers final: 19 residues processed: 315 average time/residue: 0.4897 time to fit residues: 181.9713 Evaluate side-chains 281 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 252 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 222 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN ** C 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.197517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157798 restraints weight = 25025.198| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.68 r_work: 0.3559 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23604 Z= 0.159 Angle : 0.726 11.061 31704 Z= 0.347 Chirality : 0.042 0.226 3460 Planarity : 0.005 0.080 3756 Dihedral : 23.990 179.048 5892 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.28 % Favored : 91.37 % Rotamer: Outliers : 1.85 % Allowed : 19.28 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -0.57 (0.17), residues: 2560 helix: 0.87 (0.14), residues: 1476 sheet: -1.42 (0.64), residues: 76 loop : -2.27 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.018 0.002 TYR D 657 PHE 0.016 0.001 PHE A 341 TRP 0.015 0.002 TRP A 733 HIS 0.008 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (23600) covalent geometry : angle 0.72582 / 0.35 (31696) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 0.79510 / 0.43 ( 8) hydrogen bonds : bond 0.03518 / 2.32 ( 955) hydrogen bonds : angle 4.18948 / 2.98 ( 2805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.7418 (mpt180) cc_final: 0.6907 (mpp80) REVERT: A 607 GLN cc_start: 0.8895 (tt0) cc_final: 0.8222 (mp10) REVERT: A 766 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7616 (tppp) REVERT: A 782 GLU cc_start: 0.8068 (tp30) cc_final: 0.7831 (mm-30) REVERT: B 274 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7782 (mm-40) REVERT: B 607 GLN cc_start: 0.8856 (tt0) cc_final: 0.8155 (mp10) REVERT: B 766 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7585 (tppp) REVERT: C 274 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: C 607 GLN cc_start: 0.8853 (tt0) cc_final: 0.8185 (mp10) REVERT: C 766 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7603 (tppp) REVERT: D 193 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6297 (p) REVERT: D 274 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: D 607 GLN cc_start: 0.8878 (tt0) cc_final: 0.8160 (mp10) REVERT: D 766 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7627 (tppp) outliers start: 42 outliers final: 21 residues processed: 292 average time/residue: 0.5414 time to fit residues: 184.1652 Evaluate side-chains 280 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 274 GLN Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 85 optimal weight: 0.9980 chunk 196 optimal weight: 0.0870 chunk 168 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 187 optimal weight: 0.1980 chunk 233 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 787 HIS D 239 GLN D 791 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.202670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164530 restraints weight = 25197.441| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.70 r_work: 0.3607 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23604 Z= 0.126 Angle : 0.707 12.932 31704 Z= 0.335 Chirality : 0.041 0.262 3460 Planarity : 0.005 0.078 3756 Dihedral : 23.662 179.562 5892 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.97 % Favored : 91.80 % Rotamer: Outliers : 1.36 % Allowed : 20.03 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -0.38 (0.17), residues: 2560 helix: 1.02 (0.14), residues: 1476 sheet: -1.58 (0.62), residues: 84 loop : -2.13 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 315 TYR 0.015 0.001 TYR A 621 PHE 0.037 0.001 PHE A 357 TRP 0.016 0.001 TRP D 737 HIS 0.008 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (23600) covalent geometry : angle 0.70705 / 0.34 (31696) SS BOND : bond 0.00114 / 0.05 ( 4) SS BOND : angle 0.78900 / 0.43 ( 8) hydrogen bonds : bond 0.03257 / 2.16 ( 955) hydrogen bonds : angle 4.13617 / 2.94 ( 2805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5120 Ramachandran restraints generated. 2560 Oldfield, 0 Emsley, 2560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 GLN cc_start: 0.8609 (tt0) cc_final: 0.8132 (mp10) REVERT: A 766 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7582 (tppp) REVERT: A 782 GLU cc_start: 0.7701 (tp30) cc_final: 0.7367 (mm-30) REVERT: B 274 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7571 (mm110) REVERT: B 607 GLN cc_start: 0.8549 (tt0) cc_final: 0.8033 (mp10) REVERT: B 766 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7539 (tppp) REVERT: C 274 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: C 607 GLN cc_start: 0.8567 (tt0) cc_final: 0.8057 (mp10) REVERT: D 274 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7549 (mm110) REVERT: D 607 GLN cc_start: 0.8634 (tt0) cc_final: 0.8087 (mp10) outliers start: 31 outliers final: 18 residues processed: 285 average time/residue: 0.5247 time to fit residues: 174.5265 Evaluate side-chains 279 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 782 GLU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 274 GLN Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 187 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 253 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.201643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163727 restraints weight = 25147.106| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.66 r_work: 0.3573 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23604 Z= 0.132 Angle : 0.717 11.852 31704 Z= 0.340 Chirality : 0.041 0.271 3460 Planarity : 0.005 0.079 3756 Dihedral : 23.412 179.060 5892 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.05 % Favored : 91.64 % Rotamer: Outliers : 1.23 % Allowed : 20.33 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -0.36 (0.17), residues: 2560 helix: 1.05 (0.14), residues: 1472 sheet: -1.40 (0.66), residues: 68 loop : -2.16 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 316 TYR 0.017 0.001 TYR A 621 PHE 0.028 0.001 PHE A 357 TRP 0.015 0.002 TRP A 733 HIS 0.008 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (23600) covalent geometry : angle 0.71654 / 0.34 (31696) SS BOND : bond 0.00106 / 0.05 ( 4) SS BOND : angle 0.79376 / 0.43 ( 8) hydrogen bonds : bond 0.03277 / 2.17 ( 955) hydrogen bonds : angle 4.14616 / 2.94 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6075.41 seconds wall clock time: 104 minutes 26.53 seconds (6266.53 seconds total)