Starting phenix.real_space_refine on Tue Sep 15 01:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wlb_21820/09_2026/6wlb_21820.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wlb_21820/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6wlb_21820/09_2026/6wlb_21820.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wlb_21820/09_2026/6wlb_21820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wlb_21820/09_2026/6wlb_21820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wlb_21820/09_2026/6wlb_21820.map" model { file = "/net/cci-nas-00/data/ceres_data/6wlb_21820/09_2026/6wlb_21820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wlb_21820/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 chiralities: 4 Time building chain proxies: 5.56, per 1000 atoms: 0.16 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: 3.18 Conformation dependent library (CDL) restraints added in 859.2 milliseconds 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: 0.82 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: 7.81 Time building geometry restraints manager: 4.26 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: 14955 17.62 - 35.24: 1130 35.24 - 52.86: 289 52.86 - 70.48: 106 70.48 - 88.10: 6 Dihedral angle restraints: 16486 sinusoidal: 8779 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 16483 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: 0.010 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.380 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 13.084 88.098 6426 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/Z covalent geometry : bond 0.00466 / 0.23 (17985) covalent geometry : angle 0.56808 / 0.29 (24465) hydrogen bonds : bond 0.14251 / 9.32 ( 910) hydrogen bonds : angle 5.52719 / 3.95 ( 2694) link_BETA1-4 : bond 0.00079 / 0.06 ( 12) link_BETA1-4 : angle 0.62750 / 0.45 ( 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 : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.2792 time to fit residues: 130.9439 Evaluate side-chains 255 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4287 r_free = 0.4287 target = 0.184842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145309 restraints weight = 72990.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.149827 restraints weight = 31399.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150784 restraints weight = 21535.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151410 restraints weight = 17414.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151518 restraints weight = 16686.113| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17997 Z= 0.185 Angle : 0.580 11.599 24501 Z= 0.308 Chirality : 0.063 1.460 2724 Planarity : 0.005 0.077 3054 Dihedral : 3.546 17.686 2352 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % 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: 1.00 (0.19), residues: 2142 helix: 2.06 (0.15), residues: 1188 sheet: -1.17 (0.35), residues: 162 loop : -1.14 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 537 TYR 0.019 0.002 TYR A 670 PHE 0.021 0.001 PHE A 924 TRP 0.013 0.001 TRP C 314 HIS 0.012 0.001 HIS C 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (17985) covalent geometry : angle 0.57806 / 0.31 (24465) hydrogen bonds : bond 0.04501 / 2.96 ( 910) hydrogen bonds : angle 4.44244 / 3.18 ( 2694) link_BETA1-4 : bond 0.00218 / 0.15 ( 12) link_BETA1-4 : angle 1.34399 / 0.90 ( 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 282 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 647 GLU cc_start: 0.7955 (tp30) cc_final: 0.7620 (tp30) REVERT: A 878 PRO cc_start: 0.7903 (Cg_exo) cc_final: 0.7550 (Cg_endo) REVERT: C 215 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7503 (t80) REVERT: C 647 GLU cc_start: 0.8019 (tp30) cc_final: 0.7785 (tp30) REVERT: B 215 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 647 GLU cc_start: 0.7984 (tp30) cc_final: 0.7773 (tp30) outliers start: 16 outliers final: 11 residues processed: 274 average time/residue: 0.2910 time to fit residues: 125.2888 Evaluate side-chains 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 793 LEU 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: 1.9990 chunk 52 optimal weight: 0.2980 chunk 143 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 70 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4296 r_free = 0.4296 target = 0.186013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146581 restraints weight = 72269.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.149913 restraints weight = 31407.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151778 restraints weight = 21224.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152397 restraints weight = 17146.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152998 restraints weight = 16881.329| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17997 Z= 0.113 Angle : 0.525 11.571 24501 Z= 0.275 Chirality : 0.061 1.449 2724 Planarity : 0.004 0.046 3054 Dihedral : 3.465 17.226 2352 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.96 % Allowed : 7.21 % Favored : 91.83 % 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: 1.11 (0.19), residues: 2142 helix: 2.14 (0.15), residues: 1191 sheet: -1.10 (0.35), residues: 162 loop : -1.08 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 508 TYR 0.012 0.001 TYR B 756 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/Z covalent geometry : bond 0.00255 / 0.11 (17985) covalent geometry : angle 0.52301 / 0.27 (24465) hydrogen bonds : bond 0.04287 / 2.80 ( 910) hydrogen bonds : angle 4.23810 / 3.02 ( 2694) link_BETA1-4 : bond 0.00227 / 0.14 ( 12) link_BETA1-4 : angle 1.22383 / 0.82 ( 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 273 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7899 (pt) cc_final: 0.7194 (tp) REVERT: C 215 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7569 (t80) REVERT: C 647 GLU cc_start: 0.8034 (tp30) cc_final: 0.7746 (tp30) REVERT: C 737 TYR cc_start: 0.7742 (m-80) cc_final: 0.7458 (m-10) REVERT: B 215 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7728 (t80) REVERT: B 329 GLU cc_start: 0.8576 (tp30) cc_final: 0.8326 (tp30) REVERT: B 796 PHE cc_start: 0.7415 (m-80) cc_final: 0.6602 (m-10) outliers start: 18 outliers final: 14 residues processed: 262 average time/residue: 0.2930 time to fit residues: 120.6228 Evaluate side-chains 259 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 191 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN B 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120955 restraints weight = 67103.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122327 restraints weight = 38739.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123641 restraints weight = 29133.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125161 restraints weight = 22998.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125132 restraints weight = 20832.195| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17997 Z= 0.177 Angle : 0.560 11.645 24501 Z= 0.295 Chirality : 0.063 1.480 2724 Planarity : 0.005 0.067 3054 Dihedral : 3.632 19.217 2352 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.23 % Allowed : 7.96 % Favored : 90.81 % 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: 0.94 (0.18), residues: 2142 helix: 2.05 (0.15), residues: 1191 sheet: -1.26 (0.35), residues: 165 loop : -1.21 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 425 TYR 0.013 0.001 TYR B 756 PHE 0.012 0.001 PHE B 893 TRP 0.014 0.001 TRP C 314 HIS 0.004 0.001 HIS C 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (17985) covalent geometry : angle 0.55768 / 0.29 (24465) hydrogen bonds : bond 0.04237 / 2.81 ( 910) hydrogen bonds : angle 4.23965 / 3.03 ( 2694) link_BETA1-4 : bond 0.00210 / 0.12 ( 12) link_BETA1-4 : angle 1.34553 / 0.93 ( 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 275 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8061 (pt) cc_final: 0.7418 (tp) REVERT: A 647 GLU cc_start: 0.8012 (tp30) cc_final: 0.7763 (tp30) REVERT: C 215 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7591 (t80) REVERT: C 354 MET cc_start: 0.7215 (tpp) cc_final: 0.7009 (tpp) REVERT: B 215 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 329 GLU cc_start: 0.8559 (tp30) cc_final: 0.8344 (tp30) outliers start: 23 outliers final: 15 residues processed: 263 average time/residue: 0.2886 time to fit residues: 119.0599 Evaluate side-chains 253 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 805 LEU Chi-restraints excluded: chain C residue 817 LEU 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 768 THR 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 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: 0.6980 chunk 73 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 176 optimal weight: 0.0870 chunk 135 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 441 ASN B 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.159408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121489 restraints weight = 66995.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123975 restraints weight = 35496.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125549 restraints weight = 24935.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126205 restraints weight = 21226.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126584 restraints weight = 20290.022| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17997 Z= 0.108 Angle : 0.516 11.409 24501 Z= 0.269 Chirality : 0.061 1.426 2724 Planarity : 0.004 0.052 3054 Dihedral : 3.533 16.666 2352 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.44 % Allowed : 8.65 % Favored : 89.90 % 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: 1.12 (0.19), residues: 2142 helix: 2.19 (0.15), residues: 1191 sheet: -1.20 (0.34), residues: 165 loop : -1.12 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 508 TYR 0.012 0.001 TYR B 756 PHE 0.012 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/Z covalent geometry : bond 0.00251 / 0.11 (17985) covalent geometry : angle 0.51390 / 0.27 (24465) hydrogen bonds : bond 0.03807 / 2.50 ( 910) hydrogen bonds : angle 4.04730 / 2.88 ( 2694) link_BETA1-4 : bond 0.00252 / 0.17 ( 12) link_BETA1-4 : angle 1.19109 / 0.80 ( 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 274 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8127 (pt) cc_final: 0.7501 (tp) REVERT: C 215 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 354 MET cc_start: 0.7388 (tpp) cc_final: 0.7168 (tpp) REVERT: C 840 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: C 878 PRO cc_start: 0.7888 (Cg_exo) cc_final: 0.7383 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 329 GLU cc_start: 0.8515 (tp30) cc_final: 0.8267 (tp30) REVERT: B 517 MET cc_start: 0.8284 (tpt) cc_final: 0.8061 (mmm) outliers start: 27 outliers final: 18 residues processed: 262 average time/residue: 0.2968 time to fit residues: 122.8371 Evaluate side-chains 255 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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 921 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 83 optimal weight: 0.0770 chunk 175 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN A 714 GLN 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 = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120895 restraints weight = 66649.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122550 restraints weight = 34704.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123754 restraints weight = 26948.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124412 restraints weight = 22958.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124628 restraints weight = 20790.059| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17997 Z= 0.150 Angle : 0.537 11.388 24501 Z= 0.281 Chirality : 0.062 1.429 2724 Planarity : 0.004 0.055 3054 Dihedral : 3.574 18.031 2352 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.23 % Allowed : 9.35 % Favored : 89.42 % 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: 1.08 (0.18), residues: 2142 helix: 2.19 (0.15), residues: 1191 sheet: -1.26 (0.35), residues: 165 loop : -1.20 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 508 TYR 0.011 0.001 TYR B 756 PHE 0.012 0.001 PHE B 893 TRP 0.014 0.001 TRP A 314 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17985) covalent geometry : angle 0.53482 / 0.28 (24465) hydrogen bonds : bond 0.03930 / 2.59 ( 910) hydrogen bonds : angle 4.10202 / 2.92 ( 2694) link_BETA1-4 : bond 0.00189 / 0.12 ( 12) link_BETA1-4 : angle 1.33553 / 0.92 ( 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 265 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8189 (pt) cc_final: 0.7584 (tp) REVERT: A 647 GLU cc_start: 0.7947 (tp30) cc_final: 0.7682 (tp30) REVERT: C 215 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7626 (t80) REVERT: C 354 MET cc_start: 0.7507 (tpp) cc_final: 0.7263 (tpp) REVERT: C 840 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: C 878 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7457 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7518 (t80) REVERT: B 329 GLU cc_start: 0.8497 (tp30) cc_final: 0.8271 (tp30) REVERT: B 517 MET cc_start: 0.8267 (tpt) cc_final: 0.8055 (mmm) outliers start: 23 outliers final: 16 residues processed: 255 average time/residue: 0.2985 time to fit residues: 119.3896 Evaluate side-chains 253 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 872 THR Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123578 restraints weight = 66868.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123561 restraints weight = 38942.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124671 restraints weight = 32404.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125089 restraints weight = 27436.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125438 restraints weight = 24962.874| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2482 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= 0.112 Angle : 0.520 11.392 24501 Z= 0.271 Chirality : 0.061 1.426 2724 Planarity : 0.004 0.053 3054 Dihedral : 3.530 16.058 2352 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.23 % Allowed : 9.62 % 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: 1.14 (0.19), residues: 2142 helix: 2.24 (0.16), residues: 1191 sheet: -1.23 (0.35), residues: 165 loop : -1.18 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 717 TYR 0.012 0.001 TYR B 756 PHE 0.010 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/Z covalent geometry : bond 0.00263 / 0.11 (17985) covalent geometry : angle 0.51829 / 0.27 (24465) hydrogen bonds : bond 0.03697 / 2.43 ( 910) hydrogen bonds : angle 4.01443 / 2.86 ( 2694) link_BETA1-4 : bond 0.00232 / 0.15 ( 12) link_BETA1-4 : angle 1.19752 / 0.82 ( 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: 23 poor density : 234 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8129 (pt) cc_final: 0.7588 (tp) REVERT: C 215 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7581 (t80) REVERT: C 840 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: C 878 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7620 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 329 GLU cc_start: 0.8384 (tp30) cc_final: 0.8151 (tp30) outliers start: 23 outliers final: 17 residues processed: 248 average time/residue: 0.2973 time to fit residues: 115.4258 Evaluate side-chains 250 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 A residue 872 THR 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 192 optimal weight: 0.0670 chunk 208 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121730 restraints weight = 66509.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124248 restraints weight = 34788.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125568 restraints weight = 25119.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126016 restraints weight = 21006.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126254 restraints weight = 20112.554| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2584 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= 0.109 Angle : 0.519 11.395 24501 Z= 0.269 Chirality : 0.061 1.427 2724 Planarity : 0.004 0.055 3054 Dihedral : 3.498 16.162 2352 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.34 % Allowed : 9.46 % Favored : 89.21 % 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: 1.18 (0.19), residues: 2142 helix: 2.30 (0.16), residues: 1188 sheet: -1.23 (0.35), residues: 165 loop : -1.19 (0.21), residues: 789 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 0.009 0.001 PHE B 893 TRP 0.011 0.001 TRP C 314 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (17985) covalent geometry : angle 0.51749 / 0.27 (24465) hydrogen bonds : bond 0.03623 / 2.39 ( 910) hydrogen bonds : angle 3.97503 / 2.83 ( 2694) link_BETA1-4 : bond 0.00225 / 0.14 ( 12) link_BETA1-4 : angle 1.17292 / 0.80 ( 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 260 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8261 (pt) cc_final: 0.7719 (tp) REVERT: C 215 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7612 (t80) REVERT: C 714 GLN cc_start: 0.8465 (tt0) cc_final: 0.8099 (tt0) REVERT: C 840 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: C 878 PRO cc_start: 0.7987 (Cg_exo) cc_final: 0.7527 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7549 (t80) REVERT: B 329 GLU cc_start: 0.8499 (tp30) cc_final: 0.8249 (tp30) REVERT: B 787 LEU cc_start: 0.7245 (pt) cc_final: 0.6596 (tp) outliers start: 25 outliers final: 17 residues processed: 252 average time/residue: 0.3027 time to fit residues: 118.8848 Evaluate side-chains 250 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 A residue 872 THR Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 64 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118965 restraints weight = 66910.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120748 restraints weight = 34291.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122255 restraints weight = 25714.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122855 restraints weight = 22615.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122986 restraints weight = 20109.542| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2794 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= 0.171 Angle : 0.552 11.393 24501 Z= 0.290 Chirality : 0.062 1.430 2724 Planarity : 0.005 0.075 3054 Dihedral : 3.634 16.410 2352 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.23 % Allowed : 9.78 % Favored : 89.00 % 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: 1.03 (0.19), residues: 2142 helix: 2.14 (0.15), residues: 1203 sheet: -0.90 (0.37), residues: 150 loop : -1.35 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 717 TYR 0.012 0.001 TYR B 756 PHE 0.011 0.001 PHE C 310 TRP 0.015 0.001 TRP C 314 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (17985) covalent geometry : angle 0.55008 / 0.29 (24465) hydrogen bonds : bond 0.03967 / 2.62 ( 910) hydrogen bonds : angle 4.13175 / 2.95 ( 2694) link_BETA1-4 : bond 0.00204 / 0.12 ( 12) link_BETA1-4 : angle 1.42811 / 0.99 ( 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 253 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8388 (pt) cc_final: 0.7910 (tp) REVERT: C 215 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7654 (t80) REVERT: C 359 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 840 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: B 215 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7615 (t80) REVERT: B 787 LEU cc_start: 0.7245 (pt) cc_final: 0.6727 (tp) outliers start: 23 outliers final: 19 residues processed: 243 average time/residue: 0.3057 time to fit residues: 115.4803 Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 806 GLU Chi-restraints excluded: chain A residue 872 THR 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 6 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120698 restraints weight = 66711.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122302 restraints weight = 34182.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123586 restraints weight = 26138.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124020 restraints weight = 22935.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124216 restraints weight = 20706.233| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2889 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= 0.123 Angle : 0.534 11.378 24501 Z= 0.277 Chirality : 0.061 1.424 2724 Planarity : 0.005 0.060 3054 Dihedral : 3.573 15.837 2352 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.23 % Allowed : 10.10 % 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: 1.13 (0.19), residues: 2142 helix: 2.21 (0.15), residues: 1203 sheet: -0.87 (0.37), residues: 150 loop : -1.29 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 717 TYR 0.016 0.001 TYR B 455 PHE 0.011 0.001 PHE B 893 TRP 0.013 0.001 TRP A 314 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (17985) covalent geometry : angle 0.53209 / 0.28 (24465) hydrogen bonds : bond 0.03711 / 2.43 ( 910) hydrogen bonds : angle 4.03886 / 2.88 ( 2694) link_BETA1-4 : bond 0.00248 / 0.16 ( 12) link_BETA1-4 : angle 1.27730 / 0.88 ( 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 244 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8356 (pt) cc_final: 0.7913 (tp) REVERT: C 215 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 329 GLU cc_start: 0.8568 (tp30) cc_final: 0.8294 (tp30) REVERT: C 354 MET cc_start: 0.7343 (tpp) cc_final: 0.7061 (tpp) REVERT: C 837 PHE cc_start: 0.7912 (m-10) cc_final: 0.7608 (m-10) REVERT: C 840 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: B 215 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7560 (t80) REVERT: B 787 LEU cc_start: 0.7196 (pt) cc_final: 0.6689 (tp) outliers start: 23 outliers final: 18 residues processed: 238 average time/residue: 0.3038 time to fit residues: 112.5661 Evaluate side-chains 235 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 A residue 872 THR 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 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 920 HIS 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 394 ARG 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 921 LEU 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: 2.9990 chunk 113 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 55 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121561 restraints weight = 66605.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123702 restraints weight = 35222.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125065 restraints weight = 26557.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125572 restraints weight = 22342.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125872 restraints weight = 20225.952| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17997 Z= 0.100 Angle : 0.520 11.401 24501 Z= 0.269 Chirality : 0.061 1.421 2724 Planarity : 0.004 0.059 3054 Dihedral : 3.489 15.224 2352 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.01 % Allowed : 10.36 % Favored : 88.62 % 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: 2.31 (0.16), residues: 1203 sheet: -0.80 (0.36), residues: 150 loop : -1.23 (0.21), residues: 789 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 0.014 0.001 PHE A 893 TRP 0.011 0.001 TRP C 954 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (17985) covalent geometry : angle 0.51813 / 0.27 (24465) hydrogen bonds : bond 0.03492 / 2.30 ( 910) hydrogen bonds : angle 3.92171 / 2.80 ( 2694) link_BETA1-4 : bond 0.00245 / 0.16 ( 12) link_BETA1-4 : angle 1.12837 / 0.78 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5000.10 seconds wall clock time: 86 minutes 12.84 seconds (5172.84 seconds total)