Starting phenix.real_space_refine on Fri Mar 6 20:56:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wlb_21820/03_2026/6wlb_21820.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wlb_21820/03_2026/6wlb_21820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wlb_21820/03_2026/6wlb_21820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wlb_21820/03_2026/6wlb_21820.map" model { file = "/net/cci-nas-00/data/ceres_data/6wlb_21820/03_2026/6wlb_21820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wlb_21820/03_2026/6wlb_21820.cif" } resolution = 3.5 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 11421 2.51 5 N 2886 2.21 5 O 3087 1.98 5 H 16960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34441 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11428 Classifications: {'peptide': 720} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Chain: "C" Number of atoms: 11417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11417 Classifications: {'peptide': 720} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Chain: "B" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11428 Classifications: {'peptide': 720} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.04, per 1000 atoms: 0.20 Number of scatterers: 34441 At special positions: 0 Unit cell: (136.08, 128.52, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 3087 8.00 N 2886 7.00 C 11421 6.00 H 16960 1.00 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 Links applied BETA1-4 " BGC D 1 " - " BGC D 2 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " " BGC E 1 " - " BGC E 2 " " BGC E 2 " - " BGC E 3 " " BGC E 3 " - " BGC E 4 " " BGC E 4 " - " BGC E 5 " " BGC F 1 " - " BGC F 2 " " BGC F 2 " - " BGC F 3 " " BGC F 3 " - " BGC F 4 " " BGC F 4 " - " BGC F 5 " Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 58.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 170 through 194 Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.776A pdb=" N TRP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.053A pdb=" N THR A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 322 removed outlier: 3.573A pdb=" N PHE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 346 through 373 removed outlier: 3.638A pdb=" N GLU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.624A pdb=" N ALA A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.121A pdb=" N ASP A 480 " --> pdb=" O CYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.925A pdb=" N PHE A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.735A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 653 through 657 removed outlier: 4.250A pdb=" N GLU A 657 " --> pdb=" O CYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'A' and resid 707 through 728 removed outlier: 3.972A pdb=" N ARG A 711 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 759 through 774 removed outlier: 3.845A pdb=" N ALA A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 787 through 811 removed outlier: 3.552A pdb=" N ILE A 800 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 830 removed outlier: 3.661A pdb=" N LEU A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 875 through 899 removed outlier: 3.594A pdb=" N LYS A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 930 removed outlier: 4.163A pdb=" N PHE A 913 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Proline residue: A 923 - end of helix removed outlier: 3.512A pdb=" N GLY A 927 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 958 Processing helix chain 'C' and resid 170 through 194 Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.813A pdb=" N TRP C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.037A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 322 removed outlier: 3.608A pdb=" N PHE C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.621A pdb=" N SER C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 373 removed outlier: 3.633A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.572A pdb=" N ALA C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 4.065A pdb=" N ASP C 480 " --> pdb=" O CYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.830A pdb=" N PHE C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 621 through 629 removed outlier: 3.715A pdb=" N ILE C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 652 Processing helix chain 'C' and resid 653 through 657 removed outlier: 4.233A pdb=" N GLU C 657 " --> pdb=" O CYS C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 685 Processing helix chain 'C' and resid 707 through 728 removed outlier: 3.943A pdb=" N ARG C 711 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 756 through 758 No H-bonds generated for 'chain 'C' and resid 756 through 758' Processing helix chain 'C' and resid 759 through 774 removed outlier: 3.831A pdb=" N ALA C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Proline residue: C 770 - end of helix Processing helix chain 'C' and resid 787 through 811 removed outlier: 3.580A pdb=" N ILE C 800 " --> pdb=" O PHE C 796 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 830 removed outlier: 3.592A pdb=" N LEU C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 846 Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.579A pdb=" N LYS C 899 " --> pdb=" O ASP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 930 removed outlier: 4.189A pdb=" N PHE C 913 " --> pdb=" O GLY C 909 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 914 " --> pdb=" O LYS C 910 " (cutoff:3.500A) Proline residue: C 923 - end of helix Processing helix chain 'C' and resid 938 through 958 Processing helix chain 'B' and resid 170 through 194 Processing helix chain 'B' and resid 199 through 222 removed outlier: 3.663A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.641A pdb=" N LEU B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.971A pdb=" N THR B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 322 removed outlier: 3.641A pdb=" N PHE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.585A pdb=" N SER B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 373 removed outlier: 3.585A pdb=" N GLN B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.742A pdb=" N VAL B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 removed outlier: 3.921A pdb=" N ASP B 480 " --> pdb=" O CYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 removed outlier: 3.687A pdb=" N PHE B 513 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 611 through 619 Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.712A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 653 through 657 removed outlier: 4.291A pdb=" N GLU B 657 " --> pdb=" O CYS B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 685 removed outlier: 3.554A pdb=" N GLY B 680 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 728 removed outlier: 3.995A pdb=" N ARG B 711 " --> pdb=" O ASN B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 756 through 758 No H-bonds generated for 'chain 'B' and resid 756 through 758' Processing helix chain 'B' and resid 759 through 776 removed outlier: 3.887A pdb=" N ALA B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Proline residue: B 770 - end of helix removed outlier: 3.536A pdb=" N LEU B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 809 removed outlier: 3.687A pdb=" N ILE B 800 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 830 removed outlier: 3.628A pdb=" N LEU B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 870 through 875 Processing helix chain 'B' and resid 875 through 899 removed outlier: 3.890A pdb=" N LYS B 899 " --> pdb=" O ASP B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 930 removed outlier: 3.662A pdb=" N GLY B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 913 " --> pdb=" O GLY B 909 " (cutoff:3.500A) Proline residue: B 923 - end of helix removed outlier: 3.576A pdb=" N GLY B 927 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 928 " --> pdb=" O PHE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 958 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 403 removed outlier: 6.353A pdb=" N VAL A 253 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR A 290 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 255 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER A 292 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 257 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 533 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 491 removed outlier: 7.343A pdb=" N ILE A 691 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 490 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 399 through 403 removed outlier: 6.344A pdb=" N VAL C 253 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR C 290 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE C 255 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER C 292 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 257 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 533 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 463 through 464 removed outlier: 6.551A pdb=" N ARG C 495 " --> pdb=" O GLY C 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 487 through 491 removed outlier: 7.354A pdb=" N ILE C 691 " --> pdb=" O CYS C 488 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 490 " --> pdb=" O ILE C 691 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 164 removed outlier: 3.702A pdb=" N ILE B 161 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 403 removed outlier: 6.107A pdb=" N ASP B 254 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 459 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 256 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS B 533 " --> pdb=" O ASN B 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 463 through 464 removed outlier: 6.574A pdb=" N ARG B 495 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 487 through 491 removed outlier: 7.534A pdb=" N ILE B 691 " --> pdb=" O CYS B 488 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 490 " --> pdb=" O ILE B 691 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2694 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: 8.85 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16921 1.03 - 1.23: 41 1.23 - 1.42: 7631 1.42 - 1.62: 10217 1.62 - 1.82: 135 Bond restraints: 34945 Sorted by residual: bond pdb=" C1 BGC D 5 " pdb=" O5 BGC D 5 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C1 BGC F 5 " pdb=" O5 BGC F 5 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C1 BGC E 5 " pdb=" O5 BGC E 5 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C1 BGC D 4 " pdb=" O5 BGC D 4 " ideal model delta sigma weight residual 1.408 1.502 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C1 BGC E 4 " pdb=" O5 BGC E 4 " ideal model delta sigma weight residual 1.408 1.502 -0.094 2.00e-02 2.50e+03 2.23e+01 ... (remaining 34940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.98: 62904 6.98 - 13.96: 7 13.96 - 20.94: 0 20.94 - 27.92: 28 27.92 - 34.90: 38 Bond angle restraints: 62977 Sorted by residual: angle pdb=" C LEU B 921 " pdb=" CA LEU B 921 " pdb=" HA LEU B 921 " ideal model delta sigma weight residual 109.00 74.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C LEU C 921 " pdb=" CA LEU C 921 " pdb=" HA LEU C 921 " ideal model delta sigma weight residual 109.00 74.22 34.78 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU A 921 " pdb=" CA LEU A 921 " pdb=" HA LEU A 921 " ideal model delta sigma weight residual 110.00 75.24 34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU C 921 " pdb=" CA LEU C 921 " pdb=" HA LEU C 921 " ideal model delta sigma weight residual 110.00 75.25 34.75 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C LEU A 921 " pdb=" CA LEU A 921 " pdb=" HA LEU A 921 " ideal model delta sigma weight residual 109.00 74.25 34.75 3.00e+00 1.11e-01 1.34e+02 ... (remaining 62972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 15243 17.62 - 35.24: 1134 35.24 - 52.86: 291 52.86 - 70.48: 106 70.48 - 88.10: 6 Dihedral angle restraints: 16780 sinusoidal: 9073 harmonic: 7707 Sorted by residual: dihedral pdb=" C LEU A 921 " pdb=" N LEU A 921 " pdb=" CA LEU A 921 " pdb=" CB LEU A 921 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C LEU C 921 " pdb=" N LEU C 921 " pdb=" CA LEU C 921 " pdb=" CB LEU C 921 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C LEU B 921 " pdb=" N LEU B 921 " pdb=" CA LEU B 921 " pdb=" CB LEU B 921 " ideal model delta harmonic sigma weight residual -122.60 -131.79 9.19 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 16777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.295: 2718 0.295 - 0.590: 3 0.590 - 0.884: 0 0.884 - 1.179: 0 1.179 - 1.474: 3 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CB THR C 872 " pdb=" CA THR C 872 " pdb=" OG1 THR C 872 " pdb=" CG2 THR C 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.43e+01 chirality pdb=" CB THR B 872 " pdb=" CA THR B 872 " pdb=" OG1 THR B 872 " pdb=" CG2 THR B 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.41e+01 chirality pdb=" CB THR A 872 " pdb=" CA THR A 872 " pdb=" OG1 THR A 872 " pdb=" CG2 THR A 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.40e+01 ... (remaining 2721 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 194 " -0.077 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO B 195 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 194 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO C 195 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 480 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 481 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " -0.031 5.00e-02 4.00e+02 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 91 1.92 - 2.59: 34213 2.59 - 3.26: 104125 3.26 - 3.93: 124404 3.93 - 4.60: 198179 Nonbonded interactions: 461012 Sorted by model distance: nonbonded pdb=" H ASN B 707 " pdb="HD22 ASN B 707 " model vdw 1.250 2.100 nonbonded pdb=" HA LEU B 921 " pdb=" HB3 LEU B 921 " model vdw 1.610 1.952 nonbonded pdb=" HA LEU C 921 " pdb=" HB3 LEU C 921 " model vdw 1.625 1.952 nonbonded pdb=" HA LEU A 921 " pdb=" HB3 LEU A 921 " model vdw 1.626 1.952 nonbonded pdb=" H LEU A 921 " pdb=" HA LEU A 921 " model vdw 1.641 1.816 ... (remaining 461007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 157 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA )) or resid 426 through 958)) selection = (chain 'B' and (resid 157 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA )) or resid 426 through 958)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.200 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.010 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 17997 Z= 0.228 Angle : 0.568 11.704 24501 Z= 0.292 Chirality : 0.063 1.474 2724 Planarity : 0.004 0.113 3054 Dihedral : 12.885 88.098 6720 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.16 % Allowed : 0.27 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.33 (0.19), residues: 2142 helix: 2.31 (0.16), residues: 1179 sheet: -0.81 (0.38), residues: 162 loop : -0.96 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 508 TYR 0.010 0.001 TYR A 173 PHE 0.023 0.001 PHE C 840 TRP 0.013 0.001 TRP B 954 HIS 0.003 0.000 HIS C 920 Details of bonding type rmsd covalent geometry : bond 0.00466 (17985) covalent geometry : angle 0.56808 (24465) hydrogen bonds : bond 0.14251 ( 910) hydrogen bonds : angle 5.52719 ( 2694) link_BETA1-4 : bond 0.00079 ( 12) link_BETA1-4 : angle 0.62750 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 669 ILE cc_start: 0.7896 (mm) cc_final: 0.7631 (mm) outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 0.2851 time to fit residues: 132.0913 Evaluate side-chains 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 168 ASN B 714 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.184996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142408 restraints weight = 71410.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148522 restraints weight = 31311.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.152238 restraints weight = 19351.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154455 restraints weight = 14598.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155744 restraints weight = 12393.610| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17997 Z= 0.176 Angle : 0.568 11.594 24501 Z= 0.302 Chirality : 0.063 1.461 2724 Planarity : 0.005 0.071 3054 Dihedral : 3.589 23.559 2646 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.80 % Allowed : 5.61 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.07 (0.19), residues: 2142 helix: 2.13 (0.16), residues: 1188 sheet: -1.16 (0.35), residues: 162 loop : -1.12 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 485 TYR 0.018 0.001 TYR A 670 PHE 0.018 0.001 PHE B 893 TRP 0.013 0.001 TRP C 314 HIS 0.011 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00402 (17985) covalent geometry : angle 0.56512 (24465) hydrogen bonds : bond 0.04822 ( 910) hydrogen bonds : angle 4.45759 ( 2694) link_BETA1-4 : bond 0.00260 ( 12) link_BETA1-4 : angle 1.47048 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 GLU cc_start: 0.7933 (tp30) cc_final: 0.7583 (tp30) REVERT: A 878 PRO cc_start: 0.7981 (Cg_exo) cc_final: 0.7629 (Cg_endo) REVERT: C 215 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7504 (t80) REVERT: C 647 GLU cc_start: 0.8005 (tp30) cc_final: 0.7765 (tp30) REVERT: B 647 GLU cc_start: 0.7980 (tp30) cc_final: 0.7756 (tp30) outliers start: 15 outliers final: 11 residues processed: 272 average time/residue: 0.2915 time to fit residues: 122.5444 Evaluate side-chains 259 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 921 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 147 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 640 ASN C 640 ASN B 640 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.184183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141617 restraints weight = 70840.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147755 restraints weight = 30838.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151479 restraints weight = 19057.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153724 restraints weight = 14386.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.154763 restraints weight = 12186.525| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17997 Z= 0.117 Angle : 0.524 11.591 24501 Z= 0.275 Chirality : 0.062 1.452 2724 Planarity : 0.004 0.046 3054 Dihedral : 3.404 17.342 2646 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.96 % Allowed : 6.84 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2142 helix: 2.13 (0.15), residues: 1194 sheet: -1.12 (0.35), residues: 162 loop : -1.05 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 508 TYR 0.013 0.001 TYR C 422 PHE 0.012 0.001 PHE A 924 TRP 0.011 0.001 TRP C 314 HIS 0.005 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00266 (17985) covalent geometry : angle 0.52266 (24465) hydrogen bonds : bond 0.04309 ( 910) hydrogen bonds : angle 4.22968 ( 2694) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.17153 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7827 (pt) cc_final: 0.7165 (tp) REVERT: C 215 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7554 (t80) REVERT: C 647 GLU cc_start: 0.7904 (tp30) cc_final: 0.7640 (tp30) REVERT: C 737 TYR cc_start: 0.7742 (m-80) cc_final: 0.7507 (m-10) REVERT: B 215 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 329 GLU cc_start: 0.8458 (tp30) cc_final: 0.8197 (tp30) outliers start: 18 outliers final: 13 residues processed: 260 average time/residue: 0.3041 time to fit residues: 122.8665 Evaluate side-chains 256 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 925 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 191 optimal weight: 0.3980 chunk 169 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121651 restraints weight = 67345.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124857 restraints weight = 38950.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126616 restraints weight = 26523.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127021 restraints weight = 21246.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127151 restraints weight = 20247.964| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17997 Z= 0.144 Angle : 0.535 11.637 24501 Z= 0.280 Chirality : 0.062 1.471 2724 Planarity : 0.005 0.058 3054 Dihedral : 3.506 18.379 2646 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.28 % Allowed : 7.75 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.07 (0.19), residues: 2142 helix: 2.13 (0.15), residues: 1191 sheet: -1.12 (0.35), residues: 165 loop : -1.15 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 508 TYR 0.013 0.001 TYR B 756 PHE 0.018 0.001 PHE B 893 TRP 0.013 0.001 TRP C 314 HIS 0.004 0.001 HIS C 434 Details of bonding type rmsd covalent geometry : bond 0.00336 (17985) covalent geometry : angle 0.53292 (24465) hydrogen bonds : bond 0.04047 ( 910) hydrogen bonds : angle 4.16562 ( 2694) link_BETA1-4 : bond 0.00198 ( 12) link_BETA1-4 : angle 1.25326 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7950 (pt) cc_final: 0.7297 (tp) REVERT: A 647 GLU cc_start: 0.8003 (tp30) cc_final: 0.7733 (tp30) REVERT: C 215 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7595 (t80) REVERT: C 878 PRO cc_start: 0.7943 (Cg_exo) cc_final: 0.7453 (Cg_endo) REVERT: B 215 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 329 GLU cc_start: 0.8526 (tp30) cc_final: 0.8279 (tp30) outliers start: 24 outliers final: 16 residues processed: 264 average time/residue: 0.3000 time to fit residues: 123.3594 Evaluate side-chains 255 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 115 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 196 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120705 restraints weight = 67188.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122819 restraints weight = 34642.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124073 restraints weight = 25249.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125066 restraints weight = 21720.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125161 restraints weight = 19308.169| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17997 Z= 0.150 Angle : 0.538 11.633 24501 Z= 0.282 Chirality : 0.062 1.472 2724 Planarity : 0.005 0.056 3054 Dihedral : 3.628 17.030 2646 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.44 % Allowed : 8.33 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2142 helix: 2.11 (0.15), residues: 1191 sheet: -1.28 (0.34), residues: 165 loop : -1.20 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 508 TYR 0.013 0.001 TYR B 756 PHE 0.014 0.001 PHE C 893 TRP 0.014 0.001 TRP C 314 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00353 (17985) covalent geometry : angle 0.53598 (24465) hydrogen bonds : bond 0.04072 ( 910) hydrogen bonds : angle 4.16685 ( 2694) link_BETA1-4 : bond 0.00220 ( 12) link_BETA1-4 : angle 1.36509 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8132 (pt) cc_final: 0.7514 (tp) REVERT: A 647 GLU cc_start: 0.7952 (tp30) cc_final: 0.7665 (tp30) REVERT: C 215 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7608 (t80) REVERT: C 840 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: C 878 PRO cc_start: 0.7871 (Cg_exo) cc_final: 0.7372 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 329 GLU cc_start: 0.8550 (tp30) cc_final: 0.8325 (tp30) REVERT: B 517 MET cc_start: 0.8315 (tpt) cc_final: 0.8081 (mmm) outliers start: 27 outliers final: 19 residues processed: 267 average time/residue: 0.2935 time to fit residues: 121.4495 Evaluate side-chains 261 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 714 GLN B 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119605 restraints weight = 66924.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122032 restraints weight = 33591.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123599 restraints weight = 24504.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124324 restraints weight = 21023.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124540 restraints weight = 19437.468| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17997 Z= 0.148 Angle : 0.541 11.588 24501 Z= 0.283 Chirality : 0.062 1.461 2724 Planarity : 0.005 0.053 3054 Dihedral : 3.634 17.941 2646 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.66 % Allowed : 9.19 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2142 helix: 2.10 (0.15), residues: 1203 sheet: -1.30 (0.35), residues: 165 loop : -1.19 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 508 TYR 0.013 0.001 TYR B 173 PHE 0.013 0.001 PHE B 893 TRP 0.015 0.001 TRP A 314 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00349 (17985) covalent geometry : angle 0.53894 (24465) hydrogen bonds : bond 0.03982 ( 910) hydrogen bonds : angle 4.13976 ( 2694) link_BETA1-4 : bond 0.00228 ( 12) link_BETA1-4 : angle 1.31133 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8199 (pt) cc_final: 0.7595 (tp) REVERT: C 215 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7657 (t80) REVERT: C 840 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: C 878 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7440 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7585 (t80) REVERT: B 329 GLU cc_start: 0.8549 (tp30) cc_final: 0.8308 (tp30) outliers start: 31 outliers final: 18 residues processed: 255 average time/residue: 0.2848 time to fit residues: 112.9743 Evaluate side-chains 253 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 199 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 10 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120412 restraints weight = 67161.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122675 restraints weight = 34621.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123739 restraints weight = 25725.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124954 restraints weight = 22539.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125232 restraints weight = 19991.277| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17997 Z= 0.108 Angle : 0.520 11.555 24501 Z= 0.270 Chirality : 0.061 1.453 2724 Planarity : 0.004 0.053 3054 Dihedral : 3.476 16.638 2646 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.34 % Allowed : 9.56 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.14 (0.19), residues: 2142 helix: 2.24 (0.16), residues: 1191 sheet: -1.22 (0.35), residues: 165 loop : -1.19 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 717 TYR 0.013 0.001 TYR B 756 PHE 0.010 0.001 PHE C 893 TRP 0.012 0.001 TRP C 314 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00253 (17985) covalent geometry : angle 0.51813 (24465) hydrogen bonds : bond 0.03707 ( 910) hydrogen bonds : angle 4.00866 ( 2694) link_BETA1-4 : bond 0.00257 ( 12) link_BETA1-4 : angle 1.16382 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8191 (pt) cc_final: 0.7625 (tp) REVERT: C 215 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7649 (t80) REVERT: C 840 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: C 878 PRO cc_start: 0.7896 (Cg_exo) cc_final: 0.7425 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7576 (t80) REVERT: B 329 GLU cc_start: 0.8502 (tp30) cc_final: 0.8259 (tp30) outliers start: 25 outliers final: 18 residues processed: 246 average time/residue: 0.2894 time to fit residues: 111.0924 Evaluate side-chains 248 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122292 restraints weight = 66804.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123800 restraints weight = 37259.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125093 restraints weight = 29835.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125581 restraints weight = 24585.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125853 restraints weight = 22634.403| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17997 Z= 0.119 Angle : 0.519 11.520 24501 Z= 0.270 Chirality : 0.061 1.451 2724 Planarity : 0.004 0.056 3054 Dihedral : 3.451 16.280 2646 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.34 % Allowed : 9.94 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2142 helix: 2.30 (0.16), residues: 1188 sheet: -0.77 (0.36), residues: 150 loop : -1.28 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 717 TYR 0.011 0.001 TYR B 756 PHE 0.014 0.001 PHE B 893 TRP 0.012 0.001 TRP C 314 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00282 (17985) covalent geometry : angle 0.51768 (24465) hydrogen bonds : bond 0.03671 ( 910) hydrogen bonds : angle 3.99493 ( 2694) link_BETA1-4 : bond 0.00251 ( 12) link_BETA1-4 : angle 1.19939 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8220 (pt) cc_final: 0.7675 (tp) REVERT: C 215 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7584 (t80) REVERT: C 329 GLU cc_start: 0.8449 (tp30) cc_final: 0.8234 (tp30) REVERT: C 714 GLN cc_start: 0.8345 (tt0) cc_final: 0.8047 (tt0) REVERT: C 837 PHE cc_start: 0.7615 (m-80) cc_final: 0.7390 (m-10) REVERT: C 840 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.6855 (m-80) REVERT: C 878 PRO cc_start: 0.8044 (Cg_exo) cc_final: 0.7546 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7485 (t80) REVERT: B 329 GLU cc_start: 0.8393 (tp30) cc_final: 0.8150 (tp30) outliers start: 25 outliers final: 21 residues processed: 244 average time/residue: 0.2990 time to fit residues: 113.0977 Evaluate side-chains 246 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 64 optimal weight: 1.9990 chunk 171 optimal weight: 0.4980 chunk 196 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120976 restraints weight = 66467.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123201 restraints weight = 35236.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124550 restraints weight = 26270.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125229 restraints weight = 21527.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125308 restraints weight = 20035.297| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 0.036 17997 Z= 0.119 Angle : 0.525 11.530 24501 Z= 0.273 Chirality : 0.061 1.450 2724 Planarity : 0.004 0.058 3054 Dihedral : 3.457 16.008 2646 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.23 % Allowed : 10.26 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.21 (0.19), residues: 2142 helix: 2.31 (0.16), residues: 1188 sheet: -0.79 (0.37), residues: 150 loop : -1.27 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 508 TYR 0.012 0.001 TYR B 756 PHE 0.009 0.001 PHE C 317 TRP 0.013 0.001 TRP A 314 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00283 (17985) covalent geometry : angle 0.52357 (24465) hydrogen bonds : bond 0.03648 ( 910) hydrogen bonds : angle 3.99242 ( 2694) link_BETA1-4 : bond 0.00220 ( 12) link_BETA1-4 : angle 1.18654 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8328 (pt) cc_final: 0.7793 (tp) REVERT: C 215 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7623 (t80) REVERT: C 329 GLU cc_start: 0.8581 (tp30) cc_final: 0.8360 (tp30) REVERT: C 714 GLN cc_start: 0.8480 (tt0) cc_final: 0.8098 (tt0) REVERT: C 840 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: C 878 PRO cc_start: 0.7956 (Cg_exo) cc_final: 0.7503 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7541 (t80) REVERT: B 329 GLU cc_start: 0.8512 (tp30) cc_final: 0.8256 (tp30) outliers start: 23 outliers final: 18 residues processed: 240 average time/residue: 0.2959 time to fit residues: 109.4457 Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 6 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 155 optimal weight: 0.0970 chunk 96 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120666 restraints weight = 67176.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122392 restraints weight = 33806.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123215 restraints weight = 25389.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125416 restraints weight = 22329.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125228 restraints weight = 18898.742| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17997 Z= 0.108 Angle : 0.519 11.531 24501 Z= 0.269 Chirality : 0.061 1.448 2724 Planarity : 0.004 0.074 3054 Dihedral : 3.416 17.364 2646 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.18 % Allowed : 10.15 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 2142 helix: 2.35 (0.16), residues: 1188 sheet: -0.76 (0.37), residues: 150 loop : -1.25 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 508 TYR 0.011 0.001 TYR B 756 PHE 0.015 0.001 PHE C 893 TRP 0.012 0.001 TRP A 314 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00255 (17985) covalent geometry : angle 0.51776 (24465) hydrogen bonds : bond 0.03545 ( 910) hydrogen bonds : angle 3.94371 ( 2694) link_BETA1-4 : bond 0.00235 ( 12) link_BETA1-4 : angle 1.13376 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8355 (pt) cc_final: 0.7817 (tp) REVERT: C 215 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7654 (t80) REVERT: C 329 GLU cc_start: 0.8601 (tp30) cc_final: 0.8378 (tp30) REVERT: C 714 GLN cc_start: 0.8541 (tt0) cc_final: 0.8116 (tt0) REVERT: C 840 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: C 878 PRO cc_start: 0.7874 (Cg_exo) cc_final: 0.7431 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 329 GLU cc_start: 0.8533 (tp30) cc_final: 0.8315 (tp30) REVERT: B 787 LEU cc_start: 0.7302 (pt) cc_final: 0.6609 (tp) outliers start: 22 outliers final: 18 residues processed: 237 average time/residue: 0.2971 time to fit residues: 108.4567 Evaluate side-chains 241 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 95 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120381 restraints weight = 67040.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122139 restraints weight = 34260.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123388 restraints weight = 25277.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125233 restraints weight = 21927.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125057 restraints weight = 18891.300| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17997 Z= 0.116 Angle : 0.522 11.578 24501 Z= 0.271 Chirality : 0.061 1.453 2724 Planarity : 0.004 0.060 3054 Dihedral : 3.414 15.674 2646 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.23 % Allowed : 10.42 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 2142 helix: 2.37 (0.16), residues: 1188 sheet: -0.74 (0.37), residues: 150 loop : -1.25 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 717 TYR 0.012 0.001 TYR B 756 PHE 0.009 0.001 PHE C 792 TRP 0.012 0.001 TRP A 314 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00276 (17985) covalent geometry : angle 0.52078 (24465) hydrogen bonds : bond 0.03562 ( 910) hydrogen bonds : angle 3.93808 ( 2694) link_BETA1-4 : bond 0.00218 ( 12) link_BETA1-4 : angle 1.16402 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.80 seconds wall clock time: 88 minutes 5.57 seconds (5285.57 seconds total)