Starting phenix.real_space_refine on Sat Jun 6 06:33:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y04_72384/06_2026/9y04_72384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y04_72384/06_2026/9y04_72384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y04_72384/06_2026/9y04_72384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y04_72384/06_2026/9y04_72384.map" model { file = "/net/cci-nas-00/data/ceres_data/9y04_72384/06_2026/9y04_72384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y04_72384/06_2026/9y04_72384.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 Mg 12 5.21 5 S 144 5.16 5 C 16254 2.51 5 N 4566 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25998 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "C" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "D" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "E" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "F" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.42, per 1000 atoms: 0.25 Number of scatterers: 25998 At special positions: 0 Unit cell: (143, 145, 97, 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 144 16.00 P 36 15.00 Mg 12 11.99 O 4986 8.00 N 4566 7.00 C 16254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 12 sheets defined 56.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.622A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.155A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.640A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.932A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.753A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.508A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.348A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.766A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.733A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.391A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 removed outlier: 4.200A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.162A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.526A pdb=" N ILE A 633 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.534A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 removed outlier: 4.215A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.552A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.686A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.156A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.633A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.792A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.938A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.531A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.346A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.750A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.336A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 585 removed outlier: 4.182A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 4.194A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.804A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 706 removed outlier: 3.507A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.577A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'B' and resid 762 through 766 removed outlier: 4.037A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.429A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.138A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.770A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.837A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.830A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.291A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.784A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.511A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 4.341A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 585 removed outlier: 4.220A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 4.335A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.570A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 678 removed outlier: 3.547A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.579A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.729A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.958A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.718A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.159A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.645A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.933A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.751A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.514A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.350A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.766A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.668A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.393A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 585 removed outlier: 4.207A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.527A pdb=" N ILE D 633 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 678 removed outlier: 3.524A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 removed outlier: 4.203A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.567A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.690A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.162A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.668A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.899A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.934A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.516A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.345A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 544 through 550 Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.341A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 585 removed outlier: 4.188A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 4.190A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.669A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 706 removed outlier: 3.504A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.545A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'E' and resid 762 through 766 removed outlier: 4.148A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.399A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.123A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.762A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.841A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.834A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 456 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.289A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.782A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 544 through 550 removed outlier: 3.542A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.342A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 585 removed outlier: 4.214A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 4.334A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.617A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 678 removed outlier: 3.549A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 706 removed outlier: 3.543A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.713A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing helix chain 'F' and resid 762 through 766 removed outlier: 3.782A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.474A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.645A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.422A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 241 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.667A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.634A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 241 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.629A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.429A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 241 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.627A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.665A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 241 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.647A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.633A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 241 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 543 removed outlier: 6.591A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3417 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: 4.50 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 8997 1.37 - 1.51: 7377 1.51 - 1.66: 9822 1.66 - 1.80: 174 1.80 - 1.95: 60 Bond restraints: 26430 Sorted by residual: bond pdb=" N ASP D 598 " pdb=" CA ASP D 598 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.39e-02 5.18e+03 8.64e+00 bond pdb=" N VAL D 600 " pdb=" CA VAL D 600 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.21e-02 6.83e+03 7.14e+00 bond pdb=" N GLU E 221 " pdb=" CA GLU E 221 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+00 bond pdb=" N ASN D 602 " pdb=" CA ASN D 602 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.01e+00 bond pdb=" N GLU B 221 " pdb=" CA GLU B 221 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.94e+00 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 35308 2.17 - 4.35: 386 4.35 - 6.52: 55 6.52 - 8.69: 1 8.69 - 10.87: 4 Bond angle restraints: 35754 Sorted by residual: angle pdb=" N GLY C 318 " pdb=" CA GLY C 318 " pdb=" C GLY C 318 " ideal model delta sigma weight residual 111.36 117.09 -5.73 1.17e+00 7.31e-01 2.40e+01 angle pdb=" N GLY F 318 " pdb=" CA GLY F 318 " pdb=" C GLY F 318 " ideal model delta sigma weight residual 111.36 117.02 -5.66 1.17e+00 7.31e-01 2.34e+01 angle pdb=" C MET E 219 " pdb=" N VAL E 220 " pdb=" CA VAL E 220 " ideal model delta sigma weight residual 122.97 118.28 4.69 9.80e-01 1.04e+00 2.29e+01 angle pdb=" N GLY A 318 " pdb=" CA GLY A 318 " pdb=" C GLY A 318 " ideal model delta sigma weight residual 111.36 116.80 -5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" N GLY D 318 " pdb=" CA GLY D 318 " pdb=" C GLY D 318 " ideal model delta sigma weight residual 111.36 116.78 -5.42 1.17e+00 7.31e-01 2.15e+01 ... (remaining 35749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 15540 24.05 - 48.10: 727 48.10 - 72.15: 55 72.15 - 96.20: 27 96.20 - 120.25: 1 Dihedral angle restraints: 16350 sinusoidal: 6912 harmonic: 9438 Sorted by residual: dihedral pdb=" CA ALA F 297 " pdb=" C ALA F 297 " pdb=" N PRO F 298 " pdb=" CA PRO F 298 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" O1B AGS C 903 " pdb=" O3B AGS C 903 " pdb=" PB AGS C 903 " pdb=" PG AGS C 903 " ideal model delta sinusoidal sigma weight residual 68.91 -170.84 -120.25 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 16347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2695 0.038 - 0.075: 922 0.075 - 0.113: 327 0.113 - 0.151: 75 0.151 - 0.188: 1 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CA ILE D 601 " pdb=" N ILE D 601 " pdb=" C ILE D 601 " pdb=" CB ILE D 601 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA VAL E 220 " pdb=" N VAL E 220 " pdb=" C VAL E 220 " pdb=" CB VAL E 220 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CB VAL D 600 " pdb=" CA VAL D 600 " pdb=" CG1 VAL D 600 " pdb=" CG2 VAL D 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 4017 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 599 " 0.419 9.50e-02 1.11e+02 1.88e-01 2.16e+01 pdb=" NE ARG D 599 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 599 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 599 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 599 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 596 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C ALA D 596 " 0.068 2.00e-02 2.50e+03 pdb=" O ALA D 596 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA D 597 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO F 461 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " -0.033 5.00e-02 4.00e+02 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 212 2.54 - 3.13: 20069 3.13 - 3.72: 42419 3.72 - 4.31: 59208 4.31 - 4.90: 96327 Nonbonded interactions: 218235 Sorted by model distance: nonbonded pdb="MG MG F 901 " pdb=" O3G AGS F 903 " model vdw 1.954 2.170 nonbonded pdb=" O1B AGS E 901 " pdb="MG MG E 902 " model vdw 2.000 2.170 nonbonded pdb=" O1B AGS B 901 " pdb="MG MG B 902 " model vdw 2.007 2.170 nonbonded pdb=" O2G AGS A 902 " pdb="MG MG A 904 " model vdw 2.023 2.170 nonbonded pdb=" OG1 THR F 525 " pdb="MG MG F 901 " model vdw 2.026 2.170 ... (remaining 218230 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 200 through 768) selection = (chain 'B' and resid 200 through 768) selection = (chain 'C' and resid 200 through 768) selection = (chain 'D' and resid 200 through 768) selection = (chain 'E' and resid 200 through 768) selection = (chain 'F' and resid 200 through 768) } 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.820 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:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.003 0.084 26430 Z= 0.143 Angle : 0.580 10.866 35754 Z= 0.317 Chirality : 0.043 0.188 4020 Planarity : 0.006 0.188 4668 Dihedral : 13.134 120.249 10230 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.72 % Favored : 97.06 % Rotamer: Outliers : 0.15 % Allowed : 0.11 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3270 helix: 1.11 (0.13), residues: 1770 sheet: 0.41 (0.25), residues: 378 loop : 0.47 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 638 TYR 0.010 0.001 TYR D 244 PHE 0.014 0.001 PHE C 768 TRP 0.035 0.003 TRP D 551 HIS 0.004 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (26430) covalent geometry : angle 0.58033 / 0.32 (35754) hydrogen bonds : bond 0.11644 / 8.05 ( 1198) hydrogen bonds : angle 4.59166 / 3.29 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 654 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8702 (m-30) cc_final: 0.8443 (p0) REVERT: A 205 ASP cc_start: 0.8859 (m-30) cc_final: 0.8617 (m-30) REVERT: A 239 ARG cc_start: 0.6515 (ptt180) cc_final: 0.5850 (pmm-80) REVERT: A 402 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 692 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8287 (mm-40) REVERT: B 204 ASP cc_start: 0.8774 (m-30) cc_final: 0.8380 (p0) REVERT: B 239 ARG cc_start: 0.6405 (ptt180) cc_final: 0.5964 (pmm-80) REVERT: B 244 TYR cc_start: 0.9134 (p90) cc_final: 0.8897 (p90) REVERT: B 352 SER cc_start: 0.9303 (m) cc_final: 0.9065 (p) REVERT: B 402 GLU cc_start: 0.8229 (tp30) cc_final: 0.8003 (tm-30) REVERT: B 550 MET cc_start: 0.6432 (ptt) cc_final: 0.5957 (ppp) REVERT: B 669 ASP cc_start: 0.8491 (p0) cc_final: 0.8288 (t0) REVERT: C 239 ARG cc_start: 0.6586 (ptt180) cc_final: 0.6288 (pmm-80) REVERT: C 402 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8273 (mm-30) REVERT: D 204 ASP cc_start: 0.8702 (m-30) cc_final: 0.8468 (p0) REVERT: D 205 ASP cc_start: 0.8787 (m-30) cc_final: 0.8556 (m-30) REVERT: D 239 ARG cc_start: 0.6376 (ptt180) cc_final: 0.5773 (pmm-80) REVERT: D 402 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8520 (mm-30) REVERT: D 603 GLN cc_start: 0.8613 (tp40) cc_final: 0.8400 (tt0) REVERT: D 692 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8286 (mm-40) REVERT: E 204 ASP cc_start: 0.8753 (m-30) cc_final: 0.8374 (p0) REVERT: E 239 ARG cc_start: 0.6356 (ptt180) cc_final: 0.5641 (mmt180) REVERT: E 244 TYR cc_start: 0.9162 (p90) cc_final: 0.8950 (p90) REVERT: E 352 SER cc_start: 0.9315 (m) cc_final: 0.9074 (p) REVERT: E 550 MET cc_start: 0.6368 (ptt) cc_final: 0.5917 (ppp) REVERT: F 204 ASP cc_start: 0.8772 (m-30) cc_final: 0.8568 (p0) REVERT: F 239 ARG cc_start: 0.6641 (ptt180) cc_final: 0.6273 (pmm-80) outliers start: 4 outliers final: 4 residues processed: 655 average time/residue: 0.8782 time to fit residues: 642.6031 Evaluate side-chains 333 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 329 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 226 HIS ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 568 GLN D 226 HIS ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN E 226 HIS ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN F 568 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095223 restraints weight = 39425.292| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.16 r_work: 0.3143 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26430 Z= 0.133 Angle : 0.595 12.501 35754 Z= 0.294 Chirality : 0.043 0.156 4020 Planarity : 0.006 0.060 4668 Dihedral : 8.345 122.226 3787 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.84 % Favored : 96.94 % Rotamer: Outliers : 2.16 % Allowed : 12.34 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3270 helix: 1.14 (0.13), residues: 1716 sheet: 0.44 (0.26), residues: 378 loop : 0.49 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 653 TYR 0.009 0.001 TYR F 244 PHE 0.011 0.001 PHE F 758 TRP 0.020 0.003 TRP B 551 HIS 0.009 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (26430) covalent geometry : angle 0.59542 / 0.29 (35754) hydrogen bonds : bond 0.03738 / 2.54 ( 1198) hydrogen bonds : angle 4.04727 / 2.91 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 341 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8878 (m-30) cc_final: 0.8455 (p0) REVERT: A 205 ASP cc_start: 0.8829 (m-30) cc_final: 0.8296 (m-30) REVERT: A 239 ARG cc_start: 0.6117 (ptt180) cc_final: 0.5637 (pmm-80) REVERT: A 288 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8273 (mppt) REVERT: A 692 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8233 (mm-40) REVERT: B 204 ASP cc_start: 0.8695 (m-30) cc_final: 0.8375 (p0) REVERT: B 239 ARG cc_start: 0.6279 (ptt180) cc_final: 0.6018 (pmm-80) REVERT: B 268 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9207 (tp) REVERT: B 352 SER cc_start: 0.9283 (m) cc_final: 0.9011 (p) REVERT: B 389 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8230 (pttt) REVERT: B 669 ASP cc_start: 0.8568 (p0) cc_final: 0.8297 (t0) REVERT: B 701 GLU cc_start: 0.8452 (tt0) cc_final: 0.8007 (tm-30) REVERT: C 737 GLU cc_start: 0.9003 (tt0) cc_final: 0.8638 (mt-10) REVERT: D 204 ASP cc_start: 0.8860 (m-30) cc_final: 0.8450 (p0) REVERT: D 205 ASP cc_start: 0.8847 (m-30) cc_final: 0.8345 (m-30) REVERT: D 239 ARG cc_start: 0.6310 (ptt180) cc_final: 0.5791 (pmm-80) REVERT: D 288 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8288 (mppt) REVERT: D 599 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5893 (pmt-80) REVERT: D 603 GLN cc_start: 0.8612 (tp40) cc_final: 0.8231 (tt0) REVERT: D 692 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8257 (mm-40) REVERT: D 764 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: E 204 ASP cc_start: 0.8669 (m-30) cc_final: 0.8353 (p0) REVERT: E 239 ARG cc_start: 0.6272 (ptt180) cc_final: 0.5905 (pmm-80) REVERT: E 352 SER cc_start: 0.9298 (m) cc_final: 0.9022 (p) REVERT: E 389 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8233 (pttt) REVERT: E 427 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6899 (mmp) REVERT: E 701 GLU cc_start: 0.8473 (tt0) cc_final: 0.8053 (tm-30) REVERT: F 204 ASP cc_start: 0.8772 (m-30) cc_final: 0.8487 (p0) REVERT: F 239 ARG cc_start: 0.6426 (ptt180) cc_final: 0.6153 (pmm-80) REVERT: F 295 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8712 (ptpp) REVERT: F 674 PHE cc_start: 0.8752 (t80) cc_final: 0.8507 (t80) REVERT: F 737 GLU cc_start: 0.8941 (tt0) cc_final: 0.8536 (mt-10) outliers start: 59 outliers final: 12 residues processed: 377 average time/residue: 0.7603 time to fit residues: 327.2554 Evaluate side-chains 327 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 601 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090342 restraints weight = 40161.669| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.17 r_work: 0.3121 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26430 Z= 0.225 Angle : 0.619 13.010 35754 Z= 0.304 Chirality : 0.046 0.169 4020 Planarity : 0.005 0.056 4668 Dihedral : 8.491 126.383 3780 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.09 % Rotamer: Outliers : 2.75 % Allowed : 12.38 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.15), residues: 3270 helix: 1.09 (0.13), residues: 1704 sheet: 0.26 (0.25), residues: 378 loop : 0.52 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 210 TYR 0.012 0.002 TYR F 203 PHE 0.014 0.002 PHE F 758 TRP 0.017 0.003 TRP E 551 HIS 0.006 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (26430) covalent geometry : angle 0.61852 / 0.30 (35754) hydrogen bonds : bond 0.03911 / 2.63 ( 1198) hydrogen bonds : angle 3.96446 / 2.86 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8901 (m-30) cc_final: 0.8629 (p0) REVERT: A 239 ARG cc_start: 0.6339 (ptt180) cc_final: 0.5850 (pmm-80) REVERT: A 550 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.5828 (ppp) REVERT: B 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8544 (p0) REVERT: B 239 ARG cc_start: 0.6495 (ptt180) cc_final: 0.6013 (pmm-80) REVERT: B 288 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8566 (mppt) REVERT: B 332 MET cc_start: 0.8683 (mtm) cc_final: 0.8433 (mtp) REVERT: B 352 SER cc_start: 0.9295 (m) cc_final: 0.8997 (p) REVERT: B 389 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8221 (pttt) REVERT: B 427 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6752 (mmp) REVERT: B 669 ASP cc_start: 0.8606 (p0) cc_final: 0.8383 (t0) REVERT: D 204 ASP cc_start: 0.8904 (m-30) cc_final: 0.8636 (p0) REVERT: D 239 ARG cc_start: 0.6434 (ptt180) cc_final: 0.6004 (pmm-80) REVERT: D 288 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8286 (mppt) REVERT: D 402 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8288 (mm-30) REVERT: D 599 ARG cc_start: 0.6388 (ptp90) cc_final: 0.6175 (pmt-80) REVERT: E 204 ASP cc_start: 0.8832 (m-30) cc_final: 0.8515 (p0) REVERT: E 239 ARG cc_start: 0.6488 (ptt180) cc_final: 0.5916 (pmm-80) REVERT: E 288 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8560 (mppt) REVERT: E 332 MET cc_start: 0.8641 (mtm) cc_final: 0.8407 (mtp) REVERT: E 352 SER cc_start: 0.9312 (m) cc_final: 0.9014 (p) REVERT: E 389 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8219 (pttt) REVERT: E 402 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8372 (mm-30) REVERT: E 427 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6827 (mmp) REVERT: F 204 ASP cc_start: 0.8802 (m-30) cc_final: 0.8599 (p0) REVERT: F 239 ARG cc_start: 0.6579 (ptt180) cc_final: 0.6314 (pmm-80) REVERT: F 737 GLU cc_start: 0.8960 (tt0) cc_final: 0.8696 (tp30) outliers start: 75 outliers final: 27 residues processed: 347 average time/residue: 0.7557 time to fit residues: 297.7753 Evaluate side-chains 319 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 103 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 244 optimal weight: 0.0010 chunk 266 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091688 restraints weight = 39722.963| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.17 r_work: 0.3097 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26430 Z= 0.133 Angle : 0.560 12.539 35754 Z= 0.273 Chirality : 0.043 0.138 4020 Planarity : 0.005 0.058 4668 Dihedral : 8.333 125.650 3780 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 2.60 % Allowed : 12.67 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3270 helix: 1.19 (0.13), residues: 1680 sheet: 0.16 (0.26), residues: 378 loop : 0.51 (0.20), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 210 TYR 0.010 0.001 TYR C 244 PHE 0.012 0.001 PHE F 758 TRP 0.013 0.002 TRP A 551 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (26430) covalent geometry : angle 0.56034 / 0.27 (35754) hydrogen bonds : bond 0.03403 / 2.30 ( 1198) hydrogen bonds : angle 3.86864 / 2.78 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 299 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8922 (m-30) cc_final: 0.8684 (p0) REVERT: A 239 ARG cc_start: 0.6447 (ptt180) cc_final: 0.5974 (pmm-80) REVERT: A 288 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8257 (mppt) REVERT: A 402 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8266 (mm-30) REVERT: A 603 GLN cc_start: 0.8243 (tt0) cc_final: 0.7612 (mt0) REVERT: A 678 MET cc_start: 0.7740 (ppp) cc_final: 0.7491 (ppp) REVERT: B 203 TYR cc_start: 0.7964 (m-80) cc_final: 0.7744 (m-80) REVERT: B 204 ASP cc_start: 0.8820 (m-30) cc_final: 0.8542 (p0) REVERT: B 239 ARG cc_start: 0.6354 (ptt180) cc_final: 0.6102 (pmm-80) REVERT: B 288 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8491 (mppt) REVERT: B 332 MET cc_start: 0.8680 (mtm) cc_final: 0.8432 (mtp) REVERT: B 352 SER cc_start: 0.9302 (m) cc_final: 0.9005 (p) REVERT: B 389 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8220 (pttt) REVERT: B 402 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 427 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6777 (mmp) REVERT: B 603 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8150 (mt0) REVERT: C 402 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8069 (mp0) REVERT: C 542 ILE cc_start: 0.9253 (mm) cc_final: 0.9031 (tp) REVERT: C 603 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8300 (tt0) REVERT: C 614 LYS cc_start: 0.8745 (pptt) cc_final: 0.8411 (ptmm) REVERT: D 204 ASP cc_start: 0.8904 (m-30) cc_final: 0.8679 (p0) REVERT: D 239 ARG cc_start: 0.6488 (ptt180) cc_final: 0.6111 (pmm-80) REVERT: D 288 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8366 (mppt) REVERT: D 402 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8262 (mm-30) REVERT: D 442 MET cc_start: 0.6983 (tmm) cc_final: 0.6485 (tmm) REVERT: E 204 ASP cc_start: 0.8793 (m-30) cc_final: 0.8505 (p0) REVERT: E 236 LYS cc_start: 0.7986 (tttt) cc_final: 0.7694 (tttp) REVERT: E 239 ARG cc_start: 0.6472 (ptt180) cc_final: 0.5532 (mmt180) REVERT: E 288 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8492 (mppt) REVERT: E 332 MET cc_start: 0.8635 (mtm) cc_final: 0.8387 (mtp) REVERT: E 352 SER cc_start: 0.9306 (m) cc_final: 0.9011 (p) REVERT: E 389 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8219 (pttt) REVERT: E 402 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8368 (mm-30) REVERT: E 427 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6920 (mmp) REVERT: E 603 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8169 (mt0) REVERT: F 402 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8056 (mp0) REVERT: F 542 ILE cc_start: 0.9267 (mm) cc_final: 0.9031 (tp) REVERT: F 730 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: F 737 GLU cc_start: 0.8877 (tt0) cc_final: 0.8630 (tp30) outliers start: 71 outliers final: 27 residues processed: 345 average time/residue: 0.7772 time to fit residues: 304.3671 Evaluate side-chains 318 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 268 optimal weight: 0.0270 chunk 226 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 217 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 227 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092959 restraints weight = 39668.409| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.16 r_work: 0.3121 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26430 Z= 0.111 Angle : 0.539 10.974 35754 Z= 0.262 Chirality : 0.042 0.139 4020 Planarity : 0.005 0.058 4668 Dihedral : 8.073 120.715 3780 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 2.01 % Allowed : 13.66 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3270 helix: 1.23 (0.13), residues: 1716 sheet: 0.10 (0.26), residues: 378 loop : 0.68 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 210 TYR 0.010 0.001 TYR C 244 PHE 0.010 0.001 PHE A 302 TRP 0.012 0.002 TRP A 551 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (26430) covalent geometry : angle 0.53856 / 0.26 (35754) hydrogen bonds : bond 0.03109 / 2.11 ( 1198) hydrogen bonds : angle 3.79521 / 2.73 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 294 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8942 (m-30) cc_final: 0.8688 (p0) REVERT: A 239 ARG cc_start: 0.6406 (ptt180) cc_final: 0.5987 (pmm-80) REVERT: A 288 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8230 (mppt) REVERT: A 402 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 603 GLN cc_start: 0.8267 (tt0) cc_final: 0.7634 (mt0) REVERT: B 203 TYR cc_start: 0.8113 (m-80) cc_final: 0.7846 (m-80) REVERT: B 204 ASP cc_start: 0.8814 (m-30) cc_final: 0.8516 (p0) REVERT: B 239 ARG cc_start: 0.6437 (ptt180) cc_final: 0.6163 (pmm-80) REVERT: B 288 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8511 (mppt) REVERT: B 332 MET cc_start: 0.8649 (mtm) cc_final: 0.8393 (mtp) REVERT: B 352 SER cc_start: 0.9320 (m) cc_final: 0.9030 (p) REVERT: B 389 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8216 (pttt) REVERT: B 402 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 427 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6624 (mmp) REVERT: B 603 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8128 (mt0) REVERT: C 295 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8849 (ptpp) REVERT: C 397 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 402 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8245 (mp0) REVERT: C 603 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8263 (tt0) REVERT: D 204 ASP cc_start: 0.8894 (m-30) cc_final: 0.8685 (p0) REVERT: D 239 ARG cc_start: 0.6497 (ptt180) cc_final: 0.6111 (pmm-80) REVERT: D 288 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (mppt) REVERT: D 402 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8323 (mm-30) REVERT: E 204 ASP cc_start: 0.8775 (m-30) cc_final: 0.8476 (p0) REVERT: E 210 ARG cc_start: 0.8431 (ptp90) cc_final: 0.8151 (mtm110) REVERT: E 239 ARG cc_start: 0.6372 (ptt180) cc_final: 0.6038 (pmm-80) REVERT: E 288 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8519 (mppt) REVERT: E 305 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: E 332 MET cc_start: 0.8596 (mtm) cc_final: 0.8351 (mtp) REVERT: E 352 SER cc_start: 0.9305 (m) cc_final: 0.9013 (p) REVERT: E 389 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8212 (pttt) REVERT: E 402 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 427 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6736 (mmp) REVERT: E 603 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8150 (mt0) REVERT: F 402 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8243 (mp0) REVERT: F 427 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6765 (mmp) REVERT: F 603 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8260 (tt0) REVERT: F 737 GLU cc_start: 0.8869 (tt0) cc_final: 0.8582 (tp30) outliers start: 55 outliers final: 26 residues processed: 331 average time/residue: 0.7641 time to fit residues: 287.5193 Evaluate side-chains 312 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 0.6980 chunk 222 optimal weight: 0.2980 chunk 163 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 125 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093209 restraints weight = 39767.762| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.14 r_work: 0.3120 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26430 Z= 0.117 Angle : 0.539 9.568 35754 Z= 0.261 Chirality : 0.042 0.152 4020 Planarity : 0.005 0.058 4668 Dihedral : 7.983 120.935 3780 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 2.31 % Allowed : 14.03 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3270 helix: 1.33 (0.13), residues: 1710 sheet: 0.11 (0.26), residues: 378 loop : 0.73 (0.20), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 210 TYR 0.015 0.001 TYR E 203 PHE 0.010 0.001 PHE C 758 TRP 0.012 0.002 TRP A 551 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26430) covalent geometry : angle 0.53855 / 0.26 (35754) hydrogen bonds : bond 0.03057 / 2.07 ( 1198) hydrogen bonds : angle 3.72553 / 2.68 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8906 (m-30) cc_final: 0.8689 (p0) REVERT: A 239 ARG cc_start: 0.6457 (ptt180) cc_final: 0.5959 (pmm-80) REVERT: A 288 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8223 (mppt) REVERT: A 402 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 561 GLU cc_start: 0.8400 (mp0) cc_final: 0.8127 (mp0) REVERT: A 603 GLN cc_start: 0.8342 (tt0) cc_final: 0.7705 (mt0) REVERT: B 203 TYR cc_start: 0.8259 (m-80) cc_final: 0.8025 (m-80) REVERT: B 204 ASP cc_start: 0.8819 (m-30) cc_final: 0.8555 (p0) REVERT: B 239 ARG cc_start: 0.6424 (ptt180) cc_final: 0.6175 (pmm-80) REVERT: B 288 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8523 (mppt) REVERT: B 332 MET cc_start: 0.8633 (mtm) cc_final: 0.8375 (mtp) REVERT: B 352 SER cc_start: 0.9308 (m) cc_final: 0.9023 (p) REVERT: B 427 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6606 (mmp) REVERT: B 454 TRP cc_start: 0.9100 (t-100) cc_final: 0.8895 (t-100) REVERT: B 603 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8119 (mt0) REVERT: C 295 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8860 (ptpp) REVERT: C 397 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8310 (tm-30) REVERT: C 402 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8261 (mp0) REVERT: C 427 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6781 (mmp) REVERT: C 508 MET cc_start: 0.7697 (ttt) cc_final: 0.7388 (ttm) REVERT: C 603 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8273 (tt0) REVERT: D 239 ARG cc_start: 0.6522 (ptt180) cc_final: 0.6161 (pmm-80) REVERT: D 288 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8354 (mppt) REVERT: D 402 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 442 MET cc_start: 0.7079 (tmm) cc_final: 0.6550 (tmm) REVERT: E 204 ASP cc_start: 0.8777 (m-30) cc_final: 0.8483 (p0) REVERT: E 239 ARG cc_start: 0.6344 (ptt180) cc_final: 0.6068 (pmm-80) REVERT: E 288 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8526 (mppt) REVERT: E 332 MET cc_start: 0.8590 (mtm) cc_final: 0.8343 (mtp) REVERT: E 352 SER cc_start: 0.9313 (m) cc_final: 0.9024 (p) REVERT: E 389 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8224 (pttt) REVERT: E 402 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8414 (mm-30) REVERT: E 427 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6747 (mmp) REVERT: E 603 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8136 (mt0) REVERT: F 402 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8287 (mp0) REVERT: F 427 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6811 (mmp) REVERT: F 508 MET cc_start: 0.7662 (ttt) cc_final: 0.7349 (ttm) REVERT: F 603 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8265 (tt0) REVERT: F 730 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: F 737 GLU cc_start: 0.8856 (tt0) cc_final: 0.8566 (tp30) outliers start: 63 outliers final: 33 residues processed: 333 average time/residue: 0.7439 time to fit residues: 282.4702 Evaluate side-chains 317 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 169 optimal weight: 0.7980 chunk 243 optimal weight: 0.3980 chunk 275 optimal weight: 0.6980 chunk 248 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.127955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093346 restraints weight = 39539.420| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.15 r_work: 0.3125 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26430 Z= 0.105 Angle : 0.528 9.319 35754 Z= 0.256 Chirality : 0.041 0.137 4020 Planarity : 0.005 0.058 4668 Dihedral : 7.910 120.299 3780 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 2.20 % Allowed : 14.69 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3270 helix: 1.37 (0.13), residues: 1710 sheet: 0.10 (0.26), residues: 378 loop : 0.75 (0.20), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 210 TYR 0.011 0.001 TYR D 203 PHE 0.009 0.001 PHE F 758 TRP 0.013 0.002 TRP E 454 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (26430) covalent geometry : angle 0.52774 / 0.26 (35754) hydrogen bonds : bond 0.02945 / 1.99 ( 1198) hydrogen bonds : angle 3.69943 / 2.67 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6394 (ptt180) cc_final: 0.5994 (pmm-80) REVERT: A 288 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8214 (mppt) REVERT: A 402 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8372 (mm-30) REVERT: A 603 GLN cc_start: 0.8321 (tt0) cc_final: 0.7687 (mt0) REVERT: B 203 TYR cc_start: 0.8263 (m-80) cc_final: 0.8044 (m-80) REVERT: B 204 ASP cc_start: 0.8813 (m-30) cc_final: 0.8554 (p0) REVERT: B 239 ARG cc_start: 0.6446 (ptt180) cc_final: 0.6206 (pmm-80) REVERT: B 268 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9180 (tp) REVERT: B 288 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8523 (mppt) REVERT: B 332 MET cc_start: 0.8626 (mtm) cc_final: 0.8370 (mtp) REVERT: B 352 SER cc_start: 0.9314 (m) cc_final: 0.9034 (p) REVERT: B 389 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8225 (pttt) REVERT: B 427 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6614 (mmp) REVERT: B 454 TRP cc_start: 0.9126 (t-100) cc_final: 0.8924 (t-100) REVERT: B 603 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8104 (mt0) REVERT: C 295 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8845 (ptpp) REVERT: C 397 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8317 (tm-30) REVERT: C 402 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8261 (mp0) REVERT: C 427 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6799 (mmp) REVERT: C 508 MET cc_start: 0.7710 (ttt) cc_final: 0.7371 (ttm) REVERT: C 603 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8282 (tt0) REVERT: D 239 ARG cc_start: 0.6434 (ptt180) cc_final: 0.6191 (pmm-80) REVERT: D 288 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8377 (mppt) REVERT: D 402 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 442 MET cc_start: 0.7093 (tmm) cc_final: 0.6500 (tmm) REVERT: E 204 ASP cc_start: 0.8767 (m-30) cc_final: 0.8486 (p0) REVERT: E 239 ARG cc_start: 0.6281 (ptt180) cc_final: 0.6024 (pmm-80) REVERT: E 288 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8532 (mppt) REVERT: E 332 MET cc_start: 0.8577 (mtm) cc_final: 0.8331 (mtp) REVERT: E 352 SER cc_start: 0.9308 (m) cc_final: 0.9028 (p) REVERT: E 402 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8412 (mm-30) REVERT: E 427 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6751 (mmp) REVERT: E 603 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8115 (mt0) REVERT: F 402 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8279 (mp0) REVERT: F 427 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6769 (mmp) REVERT: F 508 MET cc_start: 0.7674 (ttt) cc_final: 0.7331 (ttm) REVERT: F 603 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8270 (tt0) REVERT: F 730 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: F 737 GLU cc_start: 0.8849 (tt0) cc_final: 0.8545 (tp30) outliers start: 60 outliers final: 27 residues processed: 334 average time/residue: 0.7588 time to fit residues: 289.1059 Evaluate side-chains 310 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093184 restraints weight = 39751.923| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.14 r_work: 0.3125 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26430 Z= 0.117 Angle : 0.545 9.460 35754 Z= 0.262 Chirality : 0.042 0.136 4020 Planarity : 0.005 0.058 4668 Dihedral : 7.889 120.613 3780 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 2.20 % Allowed : 15.02 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3270 helix: 1.40 (0.13), residues: 1710 sheet: 0.12 (0.26), residues: 378 loop : 0.78 (0.20), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 210 TYR 0.015 0.001 TYR E 203 PHE 0.009 0.001 PHE C 758 TRP 0.016 0.002 TRP E 454 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (26430) covalent geometry : angle 0.54466 / 0.26 (35754) hydrogen bonds : bond 0.02961 / 2.00 ( 1198) hydrogen bonds : angle 3.67883 / 2.65 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6503 (ptt180) cc_final: 0.5994 (pmm-80) REVERT: A 288 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8208 (mppt) REVERT: A 402 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8384 (mm-30) REVERT: A 550 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.5988 (ppp) REVERT: A 561 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 603 GLN cc_start: 0.8340 (tt0) cc_final: 0.7713 (mt0) REVERT: A 669 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7994 (t0) REVERT: B 204 ASP cc_start: 0.8832 (m-30) cc_final: 0.8587 (p0) REVERT: B 239 ARG cc_start: 0.6480 (ptt180) cc_final: 0.6221 (pmm-80) REVERT: B 268 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9175 (tp) REVERT: B 288 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8515 (mppt) REVERT: B 332 MET cc_start: 0.8632 (mtm) cc_final: 0.8372 (mtp) REVERT: B 352 SER cc_start: 0.9298 (m) cc_final: 0.9007 (p) REVERT: B 427 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6656 (mmp) REVERT: B 454 TRP cc_start: 0.9129 (t-100) cc_final: 0.8905 (t-100) REVERT: B 603 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8097 (mt0) REVERT: C 397 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 427 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6817 (mmp) REVERT: C 508 MET cc_start: 0.7732 (ttt) cc_final: 0.7367 (ttm) REVERT: C 603 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8295 (tt0) REVERT: D 239 ARG cc_start: 0.6498 (ptt180) cc_final: 0.6204 (pmm-80) REVERT: D 288 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8373 (mppt) REVERT: D 402 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8385 (mm-30) REVERT: D 561 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: D 669 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.7990 (t0) REVERT: E 204 ASP cc_start: 0.8762 (m-30) cc_final: 0.8464 (p0) REVERT: E 239 ARG cc_start: 0.6430 (ptt180) cc_final: 0.6163 (pmm-80) REVERT: E 288 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8531 (mppt) REVERT: E 332 MET cc_start: 0.8595 (mtm) cc_final: 0.8347 (mtp) REVERT: E 352 SER cc_start: 0.9300 (m) cc_final: 0.9016 (p) REVERT: E 389 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8238 (pttt) REVERT: E 402 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8409 (mm-30) REVERT: E 427 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6777 (mmp) REVERT: E 603 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8098 (mt0) REVERT: F 402 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8281 (mp0) REVERT: F 427 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6772 (mmp) REVERT: F 508 MET cc_start: 0.7693 (ttt) cc_final: 0.7336 (ttm) REVERT: F 603 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8288 (tt0) REVERT: F 730 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: F 737 GLU cc_start: 0.8834 (tt0) cc_final: 0.8531 (tp30) outliers start: 60 outliers final: 30 residues processed: 320 average time/residue: 0.7536 time to fit residues: 274.5266 Evaluate side-chains 317 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 144 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 303 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 100 optimal weight: 0.0050 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092310 restraints weight = 39622.500| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.16 r_work: 0.3114 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26430 Z= 0.126 Angle : 0.557 10.047 35754 Z= 0.268 Chirality : 0.042 0.136 4020 Planarity : 0.005 0.059 4668 Dihedral : 7.926 121.140 3780 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 2.05 % Allowed : 15.42 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3270 helix: 1.40 (0.13), residues: 1710 sheet: 0.15 (0.26), residues: 378 loop : 0.79 (0.20), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 210 TYR 0.011 0.001 TYR C 244 PHE 0.010 0.001 PHE C 758 TRP 0.019 0.002 TRP E 454 HIS 0.004 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (26430) covalent geometry : angle 0.55732 / 0.27 (35754) hydrogen bonds : bond 0.03012 / 2.04 ( 1198) hydrogen bonds : angle 3.67016 / 2.65 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6433 (ptt180) cc_final: 0.6041 (pmm-80) REVERT: A 288 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8384 (mppt) REVERT: A 402 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8382 (mm-30) REVERT: A 550 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6008 (ppp) REVERT: A 561 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: A 603 GLN cc_start: 0.8370 (tt0) cc_final: 0.7736 (mt0) REVERT: A 669 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8002 (t0) REVERT: B 204 ASP cc_start: 0.8790 (m-30) cc_final: 0.8554 (p0) REVERT: B 268 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9186 (tp) REVERT: B 288 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8540 (mppt) REVERT: B 352 SER cc_start: 0.9290 (m) cc_final: 0.9006 (p) REVERT: B 389 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8305 (pttt) REVERT: B 427 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6686 (mmp) REVERT: B 454 TRP cc_start: 0.9140 (t-100) cc_final: 0.8909 (t-100) REVERT: B 603 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8100 (mt0) REVERT: C 397 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 427 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6834 (mmp) REVERT: C 508 MET cc_start: 0.7725 (ttt) cc_final: 0.7383 (ttm) REVERT: C 603 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8312 (tt0) REVERT: D 239 ARG cc_start: 0.6496 (ptt180) cc_final: 0.6227 (pmm-80) REVERT: D 288 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8371 (mppt) REVERT: D 402 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 442 MET cc_start: 0.6996 (tmm) cc_final: 0.6386 (tmm) REVERT: D 561 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: D 669 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7978 (t0) REVERT: E 204 ASP cc_start: 0.8791 (m-30) cc_final: 0.8508 (p0) REVERT: E 288 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8540 (mppt) REVERT: E 352 SER cc_start: 0.9292 (m) cc_final: 0.9008 (p) REVERT: E 389 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8301 (pttt) REVERT: E 402 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8418 (mm-30) REVERT: E 603 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8106 (mt0) REVERT: F 402 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8279 (mp0) REVERT: F 427 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6798 (mmp) REVERT: F 508 MET cc_start: 0.7738 (ttt) cc_final: 0.7392 (ttm) REVERT: F 550 MET cc_start: 0.6399 (ptp) cc_final: 0.6054 (ppp) REVERT: F 603 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8296 (tt0) REVERT: F 730 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: F 737 GLU cc_start: 0.8858 (tt0) cc_final: 0.8555 (tp30) outliers start: 56 outliers final: 30 residues processed: 321 average time/residue: 0.7642 time to fit residues: 278.8013 Evaluate side-chains 312 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 194 optimal weight: 0.0980 chunk 244 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.0070 chunk 302 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 238 optimal weight: 1.9990 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094498 restraints weight = 39675.478| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.15 r_work: 0.3135 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 26430 Z= 0.104 Angle : 0.556 9.873 35754 Z= 0.267 Chirality : 0.041 0.160 4020 Planarity : 0.005 0.061 4668 Dihedral : 7.771 119.425 3780 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Rotamer: Outliers : 1.39 % Allowed : 16.19 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3270 helix: 1.49 (0.13), residues: 1704 sheet: 0.10 (0.26), residues: 378 loop : 0.81 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 210 TYR 0.018 0.001 TYR E 203 PHE 0.011 0.001 PHE B 363 TRP 0.021 0.002 TRP F 454 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.10 (26430) covalent geometry : angle 0.55640 / 0.27 (35754) hydrogen bonds : bond 0.02786 / 1.89 ( 1198) hydrogen bonds : angle 3.64842 / 2.63 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6338 (ptt180) cc_final: 0.5973 (pmm-80) REVERT: A 288 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8221 (mppt) REVERT: A 402 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8414 (mm-30) REVERT: A 550 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6032 (ppp) REVERT: A 561 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: A 603 GLN cc_start: 0.8270 (tt0) cc_final: 0.7641 (mt0) REVERT: B 204 ASP cc_start: 0.8809 (m-30) cc_final: 0.8538 (p0) REVERT: B 288 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8491 (mppt) REVERT: B 352 SER cc_start: 0.9288 (m) cc_final: 0.8992 (p) REVERT: B 389 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8285 (pttt) REVERT: B 397 GLU cc_start: 0.8707 (tp30) cc_final: 0.8374 (tp30) REVERT: B 427 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6699 (mmp) REVERT: B 603 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8053 (mt0) REVERT: C 427 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6750 (mmp) REVERT: C 508 MET cc_start: 0.7641 (ttt) cc_final: 0.7295 (ttm) REVERT: C 603 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8277 (tt0) REVERT: D 239 ARG cc_start: 0.6313 (ptt180) cc_final: 0.6091 (pmm-80) REVERT: D 288 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8203 (mppt) REVERT: D 402 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8383 (mm-30) REVERT: D 561 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: E 204 ASP cc_start: 0.8807 (m-30) cc_final: 0.8515 (p0) REVERT: E 288 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8499 (mppt) REVERT: E 352 SER cc_start: 0.9286 (m) cc_final: 0.8991 (p) REVERT: E 389 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8270 (pttt) REVERT: E 402 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8434 (mm-30) REVERT: E 561 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8478 (mt-10) REVERT: E 603 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8056 (mt0) REVERT: F 402 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8298 (mp0) REVERT: F 427 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6767 (mmp) REVERT: F 508 MET cc_start: 0.7664 (ttt) cc_final: 0.7332 (ttm) REVERT: F 550 MET cc_start: 0.6371 (ptp) cc_final: 0.5927 (ppp) REVERT: F 603 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8255 (tt0) REVERT: F 730 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6502 (pm20) REVERT: F 737 GLU cc_start: 0.8831 (tt0) cc_final: 0.8521 (tp30) outliers start: 38 outliers final: 23 residues processed: 332 average time/residue: 0.7469 time to fit residues: 283.4423 Evaluate side-chains 310 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 730 GLU Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 218 optimal weight: 0.0270 chunk 307 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 240 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 234 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 319 optimal weight: 0.9980 chunk 130 optimal weight: 0.0370 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093418 restraints weight = 39642.274| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.18 r_work: 0.3138 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26430 Z= 0.113 Angle : 0.564 10.270 35754 Z= 0.270 Chirality : 0.042 0.169 4020 Planarity : 0.005 0.063 4668 Dihedral : 7.759 119.920 3780 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Rotamer: Outliers : 1.54 % Allowed : 16.23 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3270 helix: 1.49 (0.13), residues: 1704 sheet: 0.12 (0.26), residues: 378 loop : 0.82 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 210 TYR 0.009 0.001 TYR A 203 PHE 0.009 0.001 PHE F 758 TRP 0.025 0.002 TRP F 454 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (26430) covalent geometry : angle 0.56375 / 0.27 (35754) hydrogen bonds : bond 0.02832 / 1.92 ( 1198) hydrogen bonds : angle 3.63859 / 2.63 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9655.61 seconds wall clock time: 164 minutes 47.70 seconds (9887.70 seconds total)