Starting phenix.real_space_refine on Sat Jul 4 19:21:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1b_40958/07_2026/8t1b_40958_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1b_40958/07_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_40958/07_2026/8t1b_40958_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1b_40958/07_2026/8t1b_40958_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t1b_40958/07_2026/8t1b_40958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1b_40958/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 656 Ad-hoc single atom residues: {' NA': 4} Unusual residues: {'9ZR': 11, 'YJ0': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain breaks: 4 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: 4.98, per 1000 atoms: 0.21 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: 1.40 Conformation dependent library (CDL) restraints added in 1.0 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: 0.56 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: 3.41 Time building geometry restraints manager: 1.86 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.560 Find NCS groups from input model: 0.450 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:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- 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 : 0.686 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: 0.5311 time to fit residues: 291.0122 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 : 0.816 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.207241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166889 restraints weight = 24829.343| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.81 r_work: 0.3672 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23604 Z= 0.169 Angle : 0.792 11.646 31704 Z= 0.382 Chirality : 0.044 0.233 3460 Planarity : 0.006 0.080 3756 Dihedral : 30.273 176.899 5892 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.87 % Favored : 90.70 % Rotamer: Outliers : 2.33 % Allowed : 9.55 % Favored : 88.12 % 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: -3.35 (0.15), residues: 2560 helix: -1.39 (0.12), residues: 1484 sheet: -2.16 (0.62), residues: 76 loop : -3.48 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 779 TYR 0.021 0.001 TYR D 657 PHE 0.020 0.002 PHE B 485 TRP 0.024 0.002 TRP A 733 HIS 0.007 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (23600) covalent geometry : angle 0.79201 / 0.38 (31696) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 1.11087 / 0.60 ( 8) hydrogen bonds : bond 0.04526 / 3.02 ( 955) hydrogen bonds : angle 4.88515 / 3.43 ( 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 382 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 329 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6422 (mp0) cc_final: 0.6067 (mp0) REVERT: A 236 TYR cc_start: 0.7160 (m-80) cc_final: 0.6511 (m-80) REVERT: A 315 ARG cc_start: 0.7620 (mpt180) cc_final: 0.6944 (mpp80) REVERT: A 680 MET cc_start: 0.7645 (ptp) cc_final: 0.7441 (ptp) REVERT: B 315 ARG cc_start: 0.7171 (mpt180) cc_final: 0.6396 (mpp80) REVERT: B 350 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6591 (tp) REVERT: B 397 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: C 315 ARG cc_start: 0.7266 (mpt180) cc_final: 0.6497 (mpp80) REVERT: C 397 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: C 672 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: D 315 ARG cc_start: 0.7183 (mpt180) cc_final: 0.6424 (mpp80) REVERT: D 350 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6568 (tp) REVERT: D 397 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7861 (pm20) outliers start: 53 outliers final: 8 residues processed: 365 average time/residue: 0.4852 time to fit residues: 207.5289 Evaluate side-chains 255 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 237 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 246 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 787 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.200640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164787 restraints weight = 24980.286| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.47 r_work: 0.3609 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23604 Z= 0.169 Angle : 0.756 11.457 31704 Z= 0.361 Chirality : 0.043 0.242 3460 Planarity : 0.006 0.085 3756 Dihedral : 28.553 179.178 5892 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.71 % Favored : 90.82 % Rotamer: Outliers : 3.04 % Allowed : 13.07 % Favored : 83.89 % 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: -2.24 (0.16), residues: 2560 helix: -0.38 (0.13), residues: 1468 sheet: -2.23 (0.64), residues: 76 loop : -3.14 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 315 TYR 0.029 0.002 TYR B 657 PHE 0.023 0.002 PHE B 357 TRP 0.022 0.002 TRP A 733 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (23600) covalent geometry : angle 0.75608 / 0.36 (31696) SS BOND : bond 0.00128 / 0.06 ( 4) SS BOND : angle 0.96189 / 0.52 ( 8) hydrogen bonds : bond 0.04031 / 2.69 ( 955) hydrogen bonds : angle 4.46786 / 3.16 ( 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 371 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6463 (mp0) cc_final: 0.6175 (mp0) REVERT: A 320 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6880 (mtp85) REVERT: A 397 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: A 615 PHE cc_start: 0.7767 (m-10) cc_final: 0.6974 (t80) REVERT: B 310 LYS cc_start: 0.8180 (tttt) cc_final: 0.7964 (tttp) REVERT: B 315 ARG cc_start: 0.7340 (mpt180) cc_final: 0.6733 (mtt180) REVERT: B 607 GLN cc_start: 0.8827 (tt0) cc_final: 0.8212 (mp10) REVERT: B 685 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4461 (mmm) REVERT: C 315 ARG cc_start: 0.7319 (mpt180) cc_final: 0.6754 (mtm110) REVERT: C 607 GLN cc_start: 0.8888 (tt0) cc_final: 0.8193 (mp10) REVERT: D 315 ARG cc_start: 0.7295 (mpt180) cc_final: 0.6731 (mtt180) REVERT: D 411 TYR cc_start: 0.8421 (t80) cc_final: 0.8109 (t80) REVERT: D 607 GLN cc_start: 0.8880 (tt0) cc_final: 0.8224 (mp10) outliers start: 69 outliers final: 21 residues processed: 349 average time/residue: 0.5037 time to fit residues: 203.9590 Evaluate side-chains 266 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 614 LEU 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 417 SER Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 783 VAL 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 350 LEU 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: 0.7980 chunk 254 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 243 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4234 r_free = 0.4234 target = 0.202669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167274 restraints weight = 24995.259| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.49 r_work: 0.3635 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23604 Z= 0.134 Angle : 0.698 11.208 31704 Z= 0.334 Chirality : 0.042 0.228 3460 Planarity : 0.005 0.076 3756 Dihedral : 27.342 179.955 5892 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.36 % Favored : 91.21 % Rotamer: Outliers : 2.77 % Allowed : 14.35 % Favored : 82.88 % 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: -1.54 (0.16), residues: 2560 helix: 0.23 (0.13), residues: 1460 sheet: -2.25 (0.65), residues: 76 loop : -2.85 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.018 0.001 TYR A 657 PHE 0.014 0.001 PHE D 341 TRP 0.019 0.001 TRP A 733 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (23600) covalent geometry : angle 0.69786 / 0.33 (31696) SS BOND : bond 0.00140 / 0.06 ( 4) SS BOND : angle 0.94708 / 0.51 ( 8) hydrogen bonds : bond 0.03450 / 2.30 ( 955) hydrogen bonds : angle 4.22754 / 2.98 ( 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 341 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6414 (mp0) cc_final: 0.6094 (mp0) REVERT: B 350 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6415 (tp) REVERT: B 397 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: C 397 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: D 397 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: D 411 TYR cc_start: 0.8341 (t80) cc_final: 0.8139 (t80) outliers start: 63 outliers final: 20 residues processed: 316 average time/residue: 0.4609 time to fit residues: 171.4800 Evaluate side-chains 256 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 613 ASP Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 783 VAL 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 269 ARG 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 417 SER Chi-restraints excluded: chain D residue 504 THR 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: 20.0000 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 202 optimal weight: 0.0170 chunk 249 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 528 ASN B 260 GLN B 787 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS D 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.199753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156660 restraints weight = 24772.032| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.07 r_work: 0.3552 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23604 Z= 0.141 Angle : 0.723 11.212 31704 Z= 0.346 Chirality : 0.041 0.237 3460 Planarity : 0.005 0.085 3756 Dihedral : 26.421 179.083 5892 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.32 % Favored : 91.21 % Rotamer: Outliers : 2.68 % Allowed : 14.35 % Favored : 82.97 % 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: -1.13 (0.17), residues: 2560 helix: 0.54 (0.14), residues: 1468 sheet: -2.22 (0.66), residues: 68 loop : -2.65 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 336 TYR 0.019 0.001 TYR C 657 PHE 0.014 0.001 PHE B 485 TRP 0.018 0.002 TRP C 733 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (23600) covalent geometry : angle 0.72338 / 0.35 (31696) SS BOND : bond 0.00152 / 0.07 ( 4) SS BOND : angle 0.88616 / 0.48 ( 8) hydrogen bonds : bond 0.03501 / 2.33 ( 955) hydrogen bonds : angle 4.16047 / 2.93 ( 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 340 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6239 (mp0) cc_final: 0.5805 (mp0) REVERT: A 320 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6751 (mtp85) REVERT: A 664 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: A 766 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7651 (tppp) REVERT: B 397 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: B 534 MET cc_start: 0.5700 (tmm) cc_final: 0.5465 (tmm) REVERT: B 625 MET cc_start: 0.8462 (ttt) cc_final: 0.8242 (ttt) REVERT: B 685 MET cc_start: 0.6011 (tpt) cc_final: 0.5103 (mmm) REVERT: C 397 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: C 534 MET cc_start: 0.5714 (tmm) cc_final: 0.5421 (tmm) REVERT: C 607 GLN cc_start: 0.8697 (tt0) cc_final: 0.8152 (mp10) REVERT: D 236 TYR cc_start: 0.7131 (m-80) cc_final: 0.6665 (m-80) REVERT: D 397 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: D 411 TYR cc_start: 0.8442 (t80) cc_final: 0.8210 (t80) REVERT: D 607 GLN cc_start: 0.8706 (tt0) cc_final: 0.8106 (mp10) outliers start: 61 outliers final: 27 residues processed: 318 average time/residue: 0.5270 time to fit residues: 194.6149 Evaluate side-chains 263 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 417 SER Chi-restraints excluded: chain A residue 614 LEU 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 269 ARG 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 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 194 CYS Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 365 VAL 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: 1.9990 chunk 203 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 791 ASN B 787 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.199679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161120 restraints weight = 25080.224| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.00 r_work: 0.3561 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23604 Z= 0.149 Angle : 0.710 11.427 31704 Z= 0.338 Chirality : 0.042 0.240 3460 Planarity : 0.005 0.079 3756 Dihedral : 25.715 178.253 5892 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.12 % Favored : 91.41 % Rotamer: Outliers : 2.82 % Allowed : 15.27 % Favored : 81.91 % 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: -0.95 (0.17), residues: 2560 helix: 0.65 (0.14), residues: 1464 sheet: -1.91 (0.67), residues: 68 loop : -2.51 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 779 TYR 0.019 0.001 TYR A 657 PHE 0.015 0.001 PHE D 485 TRP 0.018 0.002 TRP A 733 HIS 0.008 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (23600) covalent geometry : angle 0.70959 / 0.34 (31696) SS BOND : bond 0.00109 / 0.05 ( 4) SS BOND : angle 0.85210 / 0.46 ( 8) hydrogen bonds : bond 0.03520 / 2.33 ( 955) hydrogen bonds : angle 4.17210 / 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 337 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6363 (mp0) cc_final: 0.5934 (mp0) REVERT: A 411 TYR cc_start: 0.8460 (t80) cc_final: 0.8231 (t80) REVERT: A 607 GLN cc_start: 0.8705 (tt0) cc_final: 0.8195 (mp10) REVERT: A 664 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5674 (pm20) REVERT: A 766 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7653 (tppp) REVERT: A 782 GLU cc_start: 0.7747 (tp30) cc_final: 0.7470 (mm-30) REVERT: B 397 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: B 607 GLN cc_start: 0.8648 (tt0) cc_final: 0.8125 (mp10) REVERT: B 766 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7585 (tppp) REVERT: C 397 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: C 607 GLN cc_start: 0.8662 (tt0) cc_final: 0.8157 (mp10) REVERT: C 615 PHE cc_start: 0.7591 (m-10) cc_final: 0.7052 (t80) REVERT: D 397 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: D 411 TYR cc_start: 0.8365 (t80) cc_final: 0.8098 (t80) REVERT: D 607 GLN cc_start: 0.8689 (tt0) cc_final: 0.8132 (mp10) REVERT: D 766 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7588 (tppp) outliers start: 64 outliers final: 28 residues processed: 310 average time/residue: 0.4917 time to fit residues: 179.0707 Evaluate side-chains 289 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 664 GLU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 783 VAL 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 613 ASP Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 783 VAL 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 194 CYS Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 365 VAL 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 613 ASP Chi-restraints excluded: chain D residue 771 THR 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: 5.9990 chunk 192 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 787 HIS ** 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 = 0.4210 r_free = 0.4210 target = 0.201747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.164030 restraints weight = 25104.983| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.68 r_work: 0.3603 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4930 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= 0.129 Angle : 0.681 11.903 31704 Z= 0.326 Chirality : 0.041 0.240 3460 Planarity : 0.005 0.078 3756 Dihedral : 24.876 178.681 5892 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.93 % Favored : 91.64 % Rotamer: Outliers : 2.38 % Allowed : 16.86 % Favored : 80.77 % 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: -0.68 (0.17), residues: 2560 helix: 0.84 (0.14), residues: 1472 sheet: -1.65 (0.66), residues: 68 loop : -2.37 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 269 TYR 0.016 0.001 TYR C 657 PHE 0.014 0.001 PHE C 341 TRP 0.016 0.001 TRP C 733 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (23600) covalent geometry : angle 0.68118 / 0.33 (31696) SS BOND : bond 0.00113 / 0.05 ( 4) SS BOND : angle 0.81665 / 0.44 ( 8) hydrogen bonds : bond 0.03345 / 2.22 ( 955) hydrogen bonds : angle 4.08548 / 2.89 ( 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: 54 poor density : 283 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 TYR cc_start: 0.8422 (t80) cc_final: 0.8203 (t80) REVERT: A 607 GLN cc_start: 0.8636 (tt0) cc_final: 0.8138 (mp10) REVERT: A 664 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5698 (pm20) REVERT: A 766 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7649 (tppp) REVERT: B 397 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: B 607 GLN cc_start: 0.8610 (tt0) cc_final: 0.8123 (mp10) REVERT: B 766 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7582 (tppp) REVERT: C 397 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: C 607 GLN cc_start: 0.8614 (tt0) cc_final: 0.8166 (mp10) REVERT: C 766 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7607 (tppp) REVERT: D 397 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: D 607 GLN cc_start: 0.8638 (tt0) cc_final: 0.8124 (mp10) REVERT: D 766 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7618 (tppp) REVERT: D 782 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7457 (tm-30) outliers start: 54 outliers final: 25 residues processed: 313 average time/residue: 0.4688 time to fit residues: 173.0233 Evaluate side-chains 295 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 664 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 223 MET 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 782 GLU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 223 MET 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 782 GLU Chi-restraints excluded: chain C residue 783 VAL 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 365 VAL 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 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: 7.9990 chunk 139 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 123 optimal weight: 0.4980 chunk 212 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 787 HIS B 791 ASN ** C 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.199163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161301 restraints weight = 25050.656| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.68 r_work: 0.3570 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23604 Z= 0.154 Angle : 0.714 11.851 31704 Z= 0.341 Chirality : 0.042 0.248 3460 Planarity : 0.005 0.080 3756 Dihedral : 24.480 177.322 5892 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.24 % Favored : 91.29 % Rotamer: Outliers : 2.46 % Allowed : 17.25 % Favored : 80.28 % 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: -0.75 (0.17), residues: 2560 helix: 0.75 (0.13), residues: 1476 sheet: -1.24 (0.68), residues: 76 loop : -2.40 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 746 TYR 0.019 0.002 TYR C 657 PHE 0.015 0.001 PHE C 341 TRP 0.017 0.002 TRP A 733 HIS 0.006 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (23600) covalent geometry : angle 0.71418 / 0.34 (31696) SS BOND : bond 0.00105 / 0.05 ( 4) SS BOND : angle 0.82921 / 0.45 ( 8) hydrogen bonds : bond 0.03559 / 2.35 ( 955) hydrogen bonds : angle 4.22068 / 2.97 ( 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 342 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 TYR cc_start: 0.8447 (t80) cc_final: 0.8195 (t80) REVERT: A 448 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7762 (pt0) REVERT: A 607 GLN cc_start: 0.8645 (tt0) cc_final: 0.8115 (mp10) REVERT: A 664 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5736 (pm20) REVERT: A 766 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7660 (tppp) REVERT: B 274 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7542 (mm-40) REVERT: B 397 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: B 607 GLN cc_start: 0.8625 (tt0) cc_final: 0.8072 (mp10) REVERT: B 766 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7605 (tppp) REVERT: C 397 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: C 607 GLN cc_start: 0.8636 (tt0) cc_final: 0.8118 (mp10) REVERT: C 615 PHE cc_start: 0.7572 (m-10) cc_final: 0.6996 (t80) REVERT: C 766 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7624 (tppp) REVERT: D 397 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: D 607 GLN cc_start: 0.8651 (tt0) cc_final: 0.8091 (mp10) outliers start: 56 outliers final: 29 residues processed: 311 average time/residue: 0.4813 time to fit residues: 175.3164 Evaluate side-chains 297 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 664 GLU 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 274 GLN 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 613 ASP 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 417 SER 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 194 CYS Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 365 VAL 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 613 ASP 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: 2.9990 chunk 13 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 222 optimal weight: 0.2980 chunk 142 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 787 HIS C 787 HIS C 791 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.197004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149987 restraints weight = 25268.574| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.84 r_work: 0.3550 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23604 Z= 0.135 Angle : 0.704 12.205 31704 Z= 0.335 Chirality : 0.042 0.242 3460 Planarity : 0.005 0.080 3756 Dihedral : 24.107 178.030 5892 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.12 % Favored : 91.45 % Rotamer: Outliers : 2.11 % Allowed : 18.31 % Favored : 79.58 % 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: -0.55 (0.17), residues: 2560 helix: 0.86 (0.14), residues: 1484 sheet: -1.39 (0.69), residues: 68 loop : -2.22 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.016 0.001 TYR D 303 PHE 0.015 0.001 PHE A 341 TRP 0.016 0.002 TRP A 733 HIS 0.007 0.001 HIS D 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (23600) covalent geometry : angle 0.70399 / 0.34 (31696) SS BOND : bond 0.00114 / 0.05 ( 4) SS BOND : angle 0.80114 / 0.44 ( 8) hydrogen bonds : bond 0.03374 / 2.23 ( 955) hydrogen bonds : angle 4.16305 / 2.94 ( 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 327 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 GLN cc_start: 0.8693 (tt0) cc_final: 0.8029 (mp10) REVERT: A 664 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: A 766 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7527 (tppp) REVERT: B 167 ASP cc_start: 0.6480 (t70) cc_final: 0.6130 (p0) REVERT: B 274 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7491 (mm-40) REVERT: B 607 GLN cc_start: 0.8660 (tt0) cc_final: 0.8028 (mp10) REVERT: B 685 MET cc_start: 0.6091 (tpt) cc_final: 0.5545 (tpt) REVERT: B 766 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7507 (tppp) REVERT: C 274 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: C 397 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: C 607 GLN cc_start: 0.8679 (tt0) cc_final: 0.8029 (mp10) REVERT: C 766 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7547 (tppp) REVERT: D 167 ASP cc_start: 0.6446 (t70) cc_final: 0.6103 (p0) REVERT: D 274 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7588 (mm-40) REVERT: D 397 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: D 607 GLN cc_start: 0.8721 (tt0) cc_final: 0.8052 (mp10) REVERT: D 625 MET cc_start: 0.8479 (ttt) cc_final: 0.8265 (ttt) REVERT: D 766 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7555 (tppp) outliers start: 48 outliers final: 24 residues processed: 307 average time/residue: 0.4496 time to fit residues: 162.1767 Evaluate side-chains 291 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 664 GLU 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 417 SER 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 274 GLN 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 783 VAL Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 613 ASP 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: 0.7980 chunk 196 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 787 HIS C 787 HIS D 550 GLN D 791 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.199029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162195 restraints weight = 25286.883| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.83 r_work: 0.3531 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5369 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= 0.146 Angle : 0.716 11.940 31704 Z= 0.342 Chirality : 0.042 0.234 3460 Planarity : 0.005 0.080 3756 Dihedral : 23.938 179.054 5892 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.93 % Favored : 91.60 % Rotamer: Outliers : 1.76 % Allowed : 19.06 % Favored : 79.18 % 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: -0.55 (0.17), residues: 2560 helix: 0.84 (0.14), residues: 1480 sheet: -1.25 (0.70), residues: 68 loop : -2.19 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 779 TYR 0.019 0.002 TYR B 621 PHE 0.015 0.001 PHE C 341 TRP 0.016 0.002 TRP A 733 HIS 0.007 0.001 HIS B 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (23600) covalent geometry : angle 0.71624 / 0.34 (31696) SS BOND : bond 0.00114 / 0.05 ( 4) SS BOND : angle 0.85854 / 0.47 ( 8) hydrogen bonds : bond 0.03468 / 2.28 ( 955) hydrogen bonds : angle 4.21794 / 2.97 ( 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 306 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 TYR cc_start: 0.8365 (t80) cc_final: 0.8146 (t80) REVERT: A 607 GLN cc_start: 0.8718 (tt0) cc_final: 0.8115 (mp10) REVERT: A 664 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.5679 (pm20) REVERT: A 766 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7600 (tppp) REVERT: A 782 GLU cc_start: 0.7725 (tp30) cc_final: 0.7062 (tp30) REVERT: B 274 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: B 607 GLN cc_start: 0.8670 (tt0) cc_final: 0.8108 (mp10) REVERT: B 766 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7628 (tppp) REVERT: C 274 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7675 (mm-40) REVERT: C 383 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7970 (mt) REVERT: C 397 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: C 607 GLN cc_start: 0.8688 (tt0) cc_final: 0.8107 (mp10) REVERT: C 615 PHE cc_start: 0.7668 (m-10) cc_final: 0.7068 (t80) REVERT: C 766 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7584 (tppp) REVERT: D 274 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7674 (mm-40) REVERT: D 383 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7924 (mt) REVERT: D 607 GLN cc_start: 0.8714 (tt0) cc_final: 0.8117 (mp10) REVERT: D 625 MET cc_start: 0.8409 (ttt) cc_final: 0.8198 (ttt) REVERT: D 766 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7596 (tppp) outliers start: 40 outliers final: 24 residues processed: 295 average time/residue: 0.5139 time to fit residues: 176.4193 Evaluate side-chains 288 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 664 GLU 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 356 LEU Chi-restraints excluded: chain B residue 417 SER 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 274 GLN Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 579 VAL 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 353 CYS Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 613 ASP 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: 0.9980 chunk 61 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 253 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 787 HIS C 239 GLN C 787 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.202197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165010 restraints weight = 25255.201| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.78 r_work: 0.3576 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23604 Z= 0.127 Angle : 0.698 12.396 31704 Z= 0.333 Chirality : 0.041 0.228 3460 Planarity : 0.005 0.078 3756 Dihedral : 23.569 179.704 5892 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.81 % Favored : 91.80 % Rotamer: Outliers : 1.58 % Allowed : 19.28 % Favored : 79.14 % 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: -0.36 (0.18), residues: 2560 helix: 0.97 (0.14), residues: 1488 sheet: -1.53 (0.56), residues: 104 loop : -2.06 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 746 TYR 0.020 0.001 TYR C 439 PHE 0.015 0.001 PHE D 707 TRP 0.016 0.001 TRP D 737 HIS 0.006 0.001 HIS C 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (23600) covalent geometry : angle 0.69818 / 0.33 (31696) SS BOND : bond 0.00114 / 0.05 ( 4) SS BOND : angle 0.82293 / 0.45 ( 8) hydrogen bonds : bond 0.03276 / 2.16 ( 955) hydrogen bonds : angle 4.12724 / 2.91 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5906.28 seconds wall clock time: 101 minutes 33.64 seconds (6093.64 seconds total)