Starting phenix.real_space_refine on Sun Jul 5 15:50:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.map" model { file = "/net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rk6_24493/07_2026/7rk6_24493.cif" } resolution = 2.91 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= 1.000 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: 7 Type Number sf(0) Gaussians Ba 8 18.26 5 K 3 8.98 5 P 4 5.49 5 S 168 5.16 5 C 18548 2.51 5 N 4700 2.21 5 O 5184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28615 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "B" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "C" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "D" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 51 Unusual residues: {' K': 3, ' BA': 2, 'PGW': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.21 Number of scatterers: 28615 At special positions: 0 Unit cell: (171.57, 171.57, 125.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ba 8 55.98 K 3 19.00 S 168 16.00 P 4 15.00 O 5184 8.00 N 4700 7.00 C 18548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 606 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6728 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 20 sheets defined 56.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 19 through 43 removed outlier: 3.891A pdb=" N SER A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.806A pdb=" N VAL A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 317 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 removed outlier: 4.229A pdb=" N ASN A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.746A pdb=" N ALA A 456 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 457 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 458 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.524A pdb=" N MET A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 removed outlier: 3.559A pdb=" N GLY A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 597 through 602 removed outlier: 3.659A pdb=" N TYR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 removed outlier: 3.752A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 4.258A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 removed outlier: 3.588A pdb=" N LEU A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 894 through 902 removed outlier: 3.856A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 902 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 940 removed outlier: 3.857A pdb=" N ASP A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 956 through 965 removed outlier: 3.603A pdb=" N GLU A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 removed outlier: 3.512A pdb=" N ALA A 980 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 981 " --> pdb=" O VAL A 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A 983 " --> pdb=" O ALA A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'B' and resid 19 through 43 removed outlier: 3.890A pdb=" N SER B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.806A pdb=" N VAL B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 317 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 removed outlier: 4.229A pdb=" N ASN B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.746A pdb=" N ALA B 456 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 457 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 458 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.523A pdb=" N MET B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 removed outlier: 3.559A pdb=" N GLY B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 540 through 550 Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.657A pdb=" N TYR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 removed outlier: 3.752A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 4.258A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 removed outlier: 3.588A pdb=" N LEU B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 894 through 902 removed outlier: 3.857A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 902 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 927 through 940 removed outlier: 3.857A pdb=" N ASP B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 938 " --> pdb=" O MET B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 956 through 965 removed outlier: 3.603A pdb=" N GLU B 960 " --> pdb=" O THR B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 removed outlier: 3.511A pdb=" N ALA B 980 " --> pdb=" O ALA B 977 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 981 " --> pdb=" O VAL B 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 983 " --> pdb=" O ALA B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'C' and resid 19 through 43 removed outlier: 3.891A pdb=" N SER C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.806A pdb=" N VAL C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 317 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 removed outlier: 4.230A pdb=" N ASN C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.746A pdb=" N ALA C 456 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 457 " --> pdb=" O ASN C 454 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 458 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.524A pdb=" N MET C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 523 removed outlier: 3.559A pdb=" N GLY C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 540 through 550 Processing helix chain 'C' and resid 592 through 597 Processing helix chain 'C' and resid 597 through 602 removed outlier: 3.659A pdb=" N TYR C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 removed outlier: 3.752A pdb=" N ALA C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 762 through 765' Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 4.258A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 removed outlier: 3.588A pdb=" N LEU C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 838 Processing helix chain 'C' and resid 839 through 851 Processing helix chain 'C' and resid 894 through 902 removed outlier: 3.856A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 902 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 927 through 940 removed outlier: 3.856A pdb=" N ASP C 931 " --> pdb=" O VAL C 927 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 938 " --> pdb=" O MET C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 952 Processing helix chain 'C' and resid 956 through 965 removed outlier: 3.604A pdb=" N GLU C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 removed outlier: 3.512A pdb=" N ALA C 980 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 981 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 983 " --> pdb=" O ALA C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1002 Processing helix chain 'C' and resid 1005 through 1018 Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.891A pdb=" N SER D 23 " --> pdb=" O PHE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 136 through 160 Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.806A pdb=" N VAL D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 317 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 removed outlier: 4.229A pdb=" N ASN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 452 through 461 removed outlier: 3.746A pdb=" N ALA D 456 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 457 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 458 " --> pdb=" O LYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.524A pdb=" N MET D 496 " --> pdb=" O PHE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 523 removed outlier: 3.559A pdb=" N GLY D 521 " --> pdb=" O ASP D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 540 through 550 Processing helix chain 'D' and resid 592 through 597 Processing helix chain 'D' and resid 597 through 602 removed outlier: 3.659A pdb=" N TYR D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 removed outlier: 3.752A pdb=" N ALA D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 762 through 765' Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 4.258A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 removed outlier: 3.588A pdb=" N LEU D 811 " --> pdb=" O ASN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 Processing helix chain 'D' and resid 839 through 851 Processing helix chain 'D' and resid 894 through 902 removed outlier: 3.856A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP D 902 " --> pdb=" O GLN D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 927 through 940 removed outlier: 3.857A pdb=" N ASP D 931 " --> pdb=" O VAL D 927 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET D 934 " --> pdb=" O LEU D 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR D 938 " --> pdb=" O MET D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 952 Processing helix chain 'D' and resid 956 through 965 removed outlier: 3.604A pdb=" N GLU D 960 " --> pdb=" O THR D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 983 removed outlier: 3.512A pdb=" N ALA D 980 " --> pdb=" O ALA D 977 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN D 981 " --> pdb=" O VAL D 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP D 983 " --> pdb=" O ALA D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1002 Processing helix chain 'D' and resid 1005 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 removed outlier: 8.353A pdb=" N GLU A 388 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 364 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 410 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 445 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 473 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 447 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.998A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 554 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.702A pdb=" N LEU A 538 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802 removed outlier: 6.689A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 741 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL A 779 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 743 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 822 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU A 891 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 824 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 387 through 388 removed outlier: 8.352A pdb=" N GLU B 388 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 364 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 410 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 445 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B 473 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 447 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.998A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 554 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.702A pdb=" N LEU B 538 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 799 through 802 removed outlier: 6.688A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 741 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 779 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 743 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS B 822 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU B 891 " --> pdb=" O CYS B 822 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 824 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 387 through 388 removed outlier: 8.353A pdb=" N GLU C 388 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE C 364 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA C 410 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 445 " --> pdb=" O ASP C 471 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL C 473 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 447 " --> pdb=" O VAL C 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.999A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 554 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.702A pdb=" N LEU C 538 " --> pdb=" O ILE C 580 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 799 through 802 removed outlier: 6.688A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL C 741 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 779 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL C 743 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 822 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU C 891 " --> pdb=" O CYS C 822 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 824 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 387 through 388 removed outlier: 8.353A pdb=" N GLU D 388 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 364 " --> pdb=" O GLU D 388 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA D 410 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 445 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL D 473 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 447 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.998A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 554 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 538 through 539 removed outlier: 3.702A pdb=" N LEU D 538 " --> pdb=" O ILE D 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 799 through 802 removed outlier: 6.689A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL D 741 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL D 779 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 743 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS D 822 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU D 891 " --> pdb=" O CYS D 822 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 824 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) 1388 hydrogen bonds defined for protein. 3708 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: 5.94 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5857 1.33 - 1.45: 6906 1.45 - 1.57: 16229 1.57 - 1.69: 4 1.69 - 1.81: 260 Bond restraints: 29256 Sorted by residual: bond pdb=" C10 PGW A1105 " pdb=" C9 PGW A1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 PGW D1105 " pdb=" C9 PGW D1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 PGW B1105 " pdb=" C9 PGW B1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 PGW C1105 " pdb=" C9 PGW C1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O14 PGW B1106 " pdb=" P PGW B1106 " ideal model delta sigma weight residual 1.512 1.731 -0.219 2.00e-02 2.50e+03 1.19e+02 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 39365 3.18 - 6.35: 259 6.35 - 9.53: 4 9.53 - 12.70: 8 12.70 - 15.88: 8 Bond angle restraints: 39644 Sorted by residual: angle pdb=" O12 PGW B1106 " pdb=" P PGW B1106 " pdb=" O13 PGW B1106 " ideal model delta sigma weight residual 111.13 127.01 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O12 PGW C1106 " pdb=" P PGW C1106 " pdb=" O13 PGW C1106 " ideal model delta sigma weight residual 111.13 126.96 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW A1106 " pdb=" P PGW A1106 " pdb=" O13 PGW A1106 " ideal model delta sigma weight residual 111.13 126.96 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW D1106 " pdb=" P PGW D1106 " pdb=" O13 PGW D1106 " ideal model delta sigma weight residual 111.13 126.96 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O13 PGW B1106 " pdb=" P PGW B1106 " pdb=" O14 PGW B1106 " ideal model delta sigma weight residual 119.81 104.03 15.78 3.00e+00 1.11e-01 2.77e+01 ... (remaining 39639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 15454 16.79 - 33.57: 1476 33.57 - 50.35: 310 50.35 - 67.14: 52 67.14 - 83.92: 24 Dihedral angle restraints: 17316 sinusoidal: 6908 harmonic: 10408 Sorted by residual: dihedral pdb=" CB CYS B 606 " pdb=" SG CYS B 606 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS C 606 " pdb=" SG CYS C 606 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -152.03 66.03 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 606 " pdb=" SG CYS A 606 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -152.02 66.02 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 17313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2543 0.028 - 0.055: 1154 0.055 - 0.083: 486 0.083 - 0.111: 235 0.111 - 0.139: 38 Chirality restraints: 4456 Sorted by residual: chirality pdb=" CA ILE C 572 " pdb=" N ILE C 572 " pdb=" C ILE C 572 " pdb=" CB ILE C 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 572 " pdb=" N ILE B 572 " pdb=" C ILE B 572 " pdb=" CB ILE B 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 572 " pdb=" N ILE A 572 " pdb=" C ILE A 572 " pdb=" CB ILE A 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 4453 not shown) Planarity restraints: 5020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B1105 " -0.039 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C10 PGW B1105 " 0.039 2.00e-02 2.50e+03 pdb=" C8 PGW B1105 " -0.039 2.00e-02 2.50e+03 pdb=" C9 PGW B1105 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A1105 " -0.039 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C10 PGW A1105 " 0.038 2.00e-02 2.50e+03 pdb=" C8 PGW A1105 " -0.039 2.00e-02 2.50e+03 pdb=" C9 PGW A1105 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C1105 " 0.039 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C10 PGW C1105 " -0.038 2.00e-02 2.50e+03 pdb=" C8 PGW C1105 " 0.039 2.00e-02 2.50e+03 pdb=" C9 PGW C1105 " -0.039 2.00e-02 2.50e+03 ... (remaining 5017 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 7907 2.80 - 3.39: 33466 3.39 - 3.97: 55474 3.97 - 4.56: 80384 4.56 - 5.14: 115137 Nonbonded interactions: 292368 Sorted by model distance: nonbonded pdb=" O VAL B 929 " pdb=" OG SER B 932 " model vdw 2.216 3.040 nonbonded pdb=" O VAL D 929 " pdb=" OG SER D 932 " model vdw 2.216 3.040 nonbonded pdb=" O VAL A 929 " pdb=" OG SER A 932 " model vdw 2.216 3.040 nonbonded pdb=" O VAL C 929 " pdb=" OG SER C 932 " model vdw 2.217 3.040 nonbonded pdb=" O LEU A 551 " pdb=" NH2 ARG A 598 " model vdw 2.222 3.120 ... (remaining 292363 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 15 through 1106) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.530 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 0.220 29260 Z= 0.271 Angle : 0.631 15.879 39652 Z= 0.302 Chirality : 0.041 0.139 4456 Planarity : 0.003 0.041 5020 Dihedral : 13.901 83.925 10576 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.15), residues: 3524 helix: 0.51 (0.13), residues: 1688 sheet: -2.48 (0.26), residues: 384 loop : -0.16 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.012 0.001 TYR C1064 PHE 0.031 0.001 PHE D 118 TRP 0.011 0.001 TRP D 789 HIS 0.003 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.27 (29256) covalent geometry : angle 0.63103 / 0.30 (39644) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.11422 / 0.06 ( 8) hydrogen bonds : bond 0.16069 / 10.77 ( 1388) hydrogen bonds : angle 6.32582 / 4.53 ( 3708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.098 Fit side-chains REVERT: A 145 PHE cc_start: 0.8094 (m-10) cc_final: 0.7877 (m-80) REVERT: A 298 MET cc_start: 0.8556 (mpp) cc_final: 0.8255 (mpp) REVERT: A 300 PHE cc_start: 0.8867 (t80) cc_final: 0.8501 (t80) REVERT: A 420 GLN cc_start: 0.7870 (mp10) cc_final: 0.7594 (tp40) REVERT: B 298 MET cc_start: 0.8562 (mpp) cc_final: 0.8259 (mpp) REVERT: B 300 PHE cc_start: 0.8869 (t80) cc_final: 0.8504 (t80) REVERT: B 420 GLN cc_start: 0.7874 (mp10) cc_final: 0.7597 (tp40) REVERT: C 145 PHE cc_start: 0.8089 (m-10) cc_final: 0.7869 (m-80) REVERT: C 298 MET cc_start: 0.8557 (mpp) cc_final: 0.8261 (mpp) REVERT: C 300 PHE cc_start: 0.8869 (t80) cc_final: 0.8502 (t80) REVERT: C 420 GLN cc_start: 0.7868 (mp10) cc_final: 0.7591 (tp40) REVERT: D 298 MET cc_start: 0.8556 (mpp) cc_final: 0.8259 (mpp) REVERT: D 300 PHE cc_start: 0.8866 (t80) cc_final: 0.8500 (t80) REVERT: D 420 GLN cc_start: 0.7867 (mp10) cc_final: 0.7591 (tp40) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.5212 time to fit residues: 176.1211 Evaluate side-chains 216 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.9980 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 406 GLN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 894 ASN C 406 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN C 460 ASN D 406 GLN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 894 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.156935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098304 restraints weight = 41107.786| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.90 r_work: 0.3293 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 29260 Z= 0.122 Angle : 0.560 7.977 39652 Z= 0.282 Chirality : 0.042 0.138 4456 Planarity : 0.004 0.042 5020 Dihedral : 7.377 86.632 3964 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.90 % Allowed : 6.98 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.15), residues: 3524 helix: 0.59 (0.13), residues: 1756 sheet: -2.18 (0.28), residues: 348 loop : -0.10 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 614 TYR 0.016 0.001 TYR B 268 PHE 0.019 0.001 PHE C 296 TRP 0.008 0.001 TRP D 391 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (29256) covalent geometry : angle 0.55978 / 0.28 (39644) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 0.06966 / 0.04 ( 8) hydrogen bonds : bond 0.03906 / 2.58 ( 1388) hydrogen bonds : angle 4.88367 / 3.49 ( 3708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9383 (m-80) cc_final: 0.8858 (m-80) REVERT: A 204 MET cc_start: 0.8764 (mtp) cc_final: 0.8530 (mtp) REVERT: A 268 TYR cc_start: 0.8517 (t80) cc_final: 0.8313 (t80) REVERT: A 298 MET cc_start: 0.8477 (mpp) cc_final: 0.8192 (mpp) REVERT: A 420 GLN cc_start: 0.8404 (mp10) cc_final: 0.7450 (tp40) REVERT: A 814 VAL cc_start: 0.7752 (m) cc_final: 0.6889 (t) REVERT: A 901 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 154 PHE cc_start: 0.9384 (m-80) cc_final: 0.8859 (m-80) REVERT: B 204 MET cc_start: 0.8769 (mtp) cc_final: 0.8536 (mtp) REVERT: B 268 TYR cc_start: 0.8517 (t80) cc_final: 0.8314 (t80) REVERT: B 298 MET cc_start: 0.8474 (mpp) cc_final: 0.8191 (mpp) REVERT: B 420 GLN cc_start: 0.8399 (mp10) cc_final: 0.7453 (tp40) REVERT: B 814 VAL cc_start: 0.7754 (m) cc_final: 0.6880 (t) REVERT: B 901 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8563 (mm) REVERT: C 154 PHE cc_start: 0.9383 (m-80) cc_final: 0.8858 (m-80) REVERT: C 204 MET cc_start: 0.8768 (mtp) cc_final: 0.8532 (mtp) REVERT: C 268 TYR cc_start: 0.8519 (t80) cc_final: 0.8314 (t80) REVERT: C 298 MET cc_start: 0.8469 (mpp) cc_final: 0.8186 (mpp) REVERT: C 420 GLN cc_start: 0.8401 (mp10) cc_final: 0.7449 (tp40) REVERT: C 814 VAL cc_start: 0.7761 (m) cc_final: 0.6891 (t) REVERT: C 901 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8563 (mm) REVERT: D 154 PHE cc_start: 0.9383 (m-80) cc_final: 0.8859 (m-80) REVERT: D 204 MET cc_start: 0.8764 (mtp) cc_final: 0.8528 (mtp) REVERT: D 268 TYR cc_start: 0.8514 (t80) cc_final: 0.8312 (t80) REVERT: D 298 MET cc_start: 0.8477 (mpp) cc_final: 0.8192 (mpp) REVERT: D 420 GLN cc_start: 0.8402 (mp10) cc_final: 0.7449 (tp40) REVERT: D 814 VAL cc_start: 0.7759 (m) cc_final: 0.6890 (t) REVERT: D 901 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8557 (mm) outliers start: 28 outliers final: 8 residues processed: 287 average time/residue: 0.4676 time to fit residues: 164.5498 Evaluate side-chains 254 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 25 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 311 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 317 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN C 894 ASN D 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.156914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097896 restraints weight = 41610.522| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.92 r_work: 0.3278 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29260 Z= 0.123 Angle : 0.546 7.683 39652 Z= 0.272 Chirality : 0.041 0.134 4456 Planarity : 0.003 0.040 5020 Dihedral : 6.915 82.806 3964 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.97 % Allowed : 9.17 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.15), residues: 3524 helix: 0.72 (0.13), residues: 1764 sheet: -2.01 (0.28), residues: 348 loop : -0.09 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 382 TYR 0.012 0.001 TYR A 268 PHE 0.023 0.001 PHE A 296 TRP 0.007 0.001 TRP A 716 HIS 0.003 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (29256) covalent geometry : angle 0.54615 / 0.27 (39644) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.10098 / 0.06 ( 8) hydrogen bonds : bond 0.03459 / 2.28 ( 1388) hydrogen bonds : angle 4.65333 / 3.33 ( 3708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9401 (m-80) cc_final: 0.8819 (m-80) REVERT: A 204 MET cc_start: 0.8821 (mtp) cc_final: 0.8561 (mtp) REVERT: A 268 TYR cc_start: 0.8441 (t80) cc_final: 0.8239 (t80) REVERT: A 298 MET cc_start: 0.8387 (mpp) cc_final: 0.8158 (mpp) REVERT: A 420 GLN cc_start: 0.8374 (mp10) cc_final: 0.7578 (tp40) REVERT: A 901 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8568 (mm) REVERT: B 154 PHE cc_start: 0.9401 (m-80) cc_final: 0.8817 (m-80) REVERT: B 204 MET cc_start: 0.8825 (mtp) cc_final: 0.8575 (mtp) REVERT: B 268 TYR cc_start: 0.8448 (t80) cc_final: 0.8244 (t80) REVERT: B 298 MET cc_start: 0.8386 (mpp) cc_final: 0.8158 (mpp) REVERT: B 420 GLN cc_start: 0.8382 (mp10) cc_final: 0.7581 (tp40) REVERT: B 901 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8571 (mm) REVERT: C 154 PHE cc_start: 0.9401 (m-80) cc_final: 0.8817 (m-80) REVERT: C 204 MET cc_start: 0.8823 (mtp) cc_final: 0.8574 (mtp) REVERT: C 268 TYR cc_start: 0.8444 (t80) cc_final: 0.8240 (t80) REVERT: C 298 MET cc_start: 0.8380 (mpp) cc_final: 0.8153 (mpp) REVERT: C 420 GLN cc_start: 0.8370 (mp10) cc_final: 0.7579 (tp40) REVERT: C 901 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8571 (mm) REVERT: D 154 PHE cc_start: 0.9401 (m-80) cc_final: 0.8817 (m-80) REVERT: D 204 MET cc_start: 0.8819 (mtp) cc_final: 0.8570 (mtp) REVERT: D 298 MET cc_start: 0.8379 (mpp) cc_final: 0.8153 (mpp) REVERT: D 420 GLN cc_start: 0.8374 (mp10) cc_final: 0.7578 (tp40) REVERT: D 901 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8567 (mm) outliers start: 30 outliers final: 13 residues processed: 289 average time/residue: 0.4614 time to fit residues: 162.8831 Evaluate side-chains 256 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 839 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 839 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 234 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 282 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 296 optimal weight: 0.0770 chunk 53 optimal weight: 4.9990 chunk 345 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.157535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098549 restraints weight = 41626.266| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.94 r_work: 0.3274 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29260 Z= 0.117 Angle : 0.541 8.216 39652 Z= 0.267 Chirality : 0.042 0.142 4456 Planarity : 0.003 0.045 5020 Dihedral : 6.611 80.607 3964 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.45 % Allowed : 10.39 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.15), residues: 3524 helix: 0.77 (0.13), residues: 1768 sheet: -1.91 (0.27), residues: 348 loop : -0.08 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 614 TYR 0.010 0.001 TYR C 268 PHE 0.022 0.001 PHE D 300 TRP 0.006 0.001 TRP A 716 HIS 0.003 0.001 HIS D 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (29256) covalent geometry : angle 0.54108 / 0.27 (39644) SS BOND : bond 0.00057 / 0.03 ( 4) SS BOND : angle 0.12882 / 0.08 ( 8) hydrogen bonds : bond 0.03277 / 2.16 ( 1388) hydrogen bonds : angle 4.57320 / 3.26 ( 3708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.9214 (ppp) cc_final: 0.8924 (pp-130) REVERT: A 154 PHE cc_start: 0.9404 (m-80) cc_final: 0.8932 (m-80) REVERT: A 173 PHE cc_start: 0.8735 (m-80) cc_final: 0.8508 (m-10) REVERT: A 204 MET cc_start: 0.8790 (mtp) cc_final: 0.8532 (mtp) REVERT: A 298 MET cc_start: 0.8381 (mpp) cc_final: 0.8122 (mpp) REVERT: A 420 GLN cc_start: 0.8414 (mp10) cc_final: 0.7581 (tp40) REVERT: A 488 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 901 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8614 (mm) REVERT: A 1064 TYR cc_start: 0.7778 (t80) cc_final: 0.7519 (t80) REVERT: B 150 MET cc_start: 0.9212 (ppp) cc_final: 0.8920 (pp-130) REVERT: B 154 PHE cc_start: 0.9404 (m-80) cc_final: 0.8932 (m-80) REVERT: B 173 PHE cc_start: 0.8739 (m-80) cc_final: 0.8510 (m-10) REVERT: B 204 MET cc_start: 0.8801 (mtp) cc_final: 0.8546 (mtp) REVERT: B 298 MET cc_start: 0.8384 (mpp) cc_final: 0.8116 (mpp) REVERT: B 420 GLN cc_start: 0.8399 (mp10) cc_final: 0.7542 (tp40) REVERT: B 488 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8449 (mm) REVERT: B 901 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 1064 TYR cc_start: 0.7776 (t80) cc_final: 0.7423 (t80) REVERT: C 150 MET cc_start: 0.9211 (ppp) cc_final: 0.8920 (pp-130) REVERT: C 154 PHE cc_start: 0.9403 (m-80) cc_final: 0.8929 (m-80) REVERT: C 173 PHE cc_start: 0.8736 (m-80) cc_final: 0.8508 (m-10) REVERT: C 204 MET cc_start: 0.8797 (mtp) cc_final: 0.8543 (mtp) REVERT: C 298 MET cc_start: 0.8374 (mpp) cc_final: 0.8109 (mpp) REVERT: C 420 GLN cc_start: 0.8392 (mp10) cc_final: 0.7540 (tp40) REVERT: C 488 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8450 (mm) REVERT: C 901 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8573 (mm) REVERT: C 1064 TYR cc_start: 0.7782 (t80) cc_final: 0.7526 (t80) REVERT: D 150 MET cc_start: 0.9212 (ppp) cc_final: 0.8923 (pp-130) REVERT: D 154 PHE cc_start: 0.9403 (m-80) cc_final: 0.8930 (m-80) REVERT: D 173 PHE cc_start: 0.8736 (m-80) cc_final: 0.8508 (m-10) REVERT: D 204 MET cc_start: 0.8795 (mtp) cc_final: 0.8540 (mtp) REVERT: D 298 MET cc_start: 0.8375 (mpp) cc_final: 0.8118 (mpp) REVERT: D 420 GLN cc_start: 0.8413 (mp10) cc_final: 0.7583 (tp40) REVERT: D 488 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8446 (mm) REVERT: D 901 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8614 (mm) REVERT: D 1064 TYR cc_start: 0.7776 (t80) cc_final: 0.7415 (t80) outliers start: 45 outliers final: 12 residues processed: 284 average time/residue: 0.4744 time to fit residues: 165.2141 Evaluate side-chains 256 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 36 optimal weight: 0.6980 chunk 306 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 240 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 224 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.156465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097359 restraints weight = 41633.214| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.91 r_work: 0.3269 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29260 Z= 0.144 Angle : 0.563 9.223 39652 Z= 0.276 Chirality : 0.042 0.172 4456 Planarity : 0.003 0.041 5020 Dihedral : 6.444 78.632 3964 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.83 % Allowed : 11.87 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.15), residues: 3524 helix: 0.87 (0.13), residues: 1756 sheet: -1.88 (0.27), residues: 348 loop : -0.02 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 614 TYR 0.011 0.001 TYR D1025 PHE 0.032 0.002 PHE D 300 TRP 0.007 0.001 TRP D 716 HIS 0.003 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (29256) covalent geometry : angle 0.56281 / 0.28 (39644) SS BOND : bond 0.00057 / 0.03 ( 4) SS BOND : angle 0.14366 / 0.07 ( 8) hydrogen bonds : bond 0.03351 / 2.20 ( 1388) hydrogen bonds : angle 4.52376 / 3.24 ( 3708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8718 (m-80) cc_final: 0.7981 (m-80) REVERT: A 173 PHE cc_start: 0.8846 (m-80) cc_final: 0.8555 (m-10) REVERT: A 204 MET cc_start: 0.8826 (mtp) cc_final: 0.8531 (mtp) REVERT: A 298 MET cc_start: 0.8441 (mpp) cc_final: 0.8179 (mpp) REVERT: A 420 GLN cc_start: 0.8403 (mp10) cc_final: 0.7583 (tp40) REVERT: A 488 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 901 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8636 (mm) REVERT: B 19 PHE cc_start: 0.8717 (m-80) cc_final: 0.7978 (m-80) REVERT: B 150 MET cc_start: 0.9209 (ppp) cc_final: 0.8878 (pp-130) REVERT: B 154 PHE cc_start: 0.9417 (m-80) cc_final: 0.8922 (m-80) REVERT: B 173 PHE cc_start: 0.8848 (m-80) cc_final: 0.8556 (m-10) REVERT: B 204 MET cc_start: 0.8830 (mtp) cc_final: 0.8538 (mtp) REVERT: B 246 GLU cc_start: 0.9003 (tp30) cc_final: 0.8750 (tp30) REVERT: B 298 MET cc_start: 0.8441 (mpp) cc_final: 0.8181 (mpp) REVERT: B 420 GLN cc_start: 0.8407 (mp10) cc_final: 0.7588 (tp40) REVERT: B 488 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8465 (mm) REVERT: B 617 LYS cc_start: 0.7905 (mmtm) cc_final: 0.7440 (mmtt) REVERT: B 901 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8639 (mm) REVERT: C 19 PHE cc_start: 0.8717 (m-80) cc_final: 0.7979 (m-80) REVERT: C 173 PHE cc_start: 0.8845 (m-80) cc_final: 0.8555 (m-10) REVERT: C 204 MET cc_start: 0.8826 (mtp) cc_final: 0.8532 (mtp) REVERT: C 246 GLU cc_start: 0.9007 (tp30) cc_final: 0.8752 (tp30) REVERT: C 298 MET cc_start: 0.8435 (mpp) cc_final: 0.8175 (mpp) REVERT: C 420 GLN cc_start: 0.8407 (mp10) cc_final: 0.7582 (tp40) REVERT: C 488 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8464 (mm) REVERT: C 901 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8636 (mm) REVERT: D 19 PHE cc_start: 0.8713 (m-80) cc_final: 0.7975 (m-80) REVERT: D 150 MET cc_start: 0.9210 (ppp) cc_final: 0.8879 (pp-130) REVERT: D 154 PHE cc_start: 0.9417 (m-80) cc_final: 0.8922 (m-80) REVERT: D 173 PHE cc_start: 0.8848 (m-80) cc_final: 0.8557 (m-10) REVERT: D 204 MET cc_start: 0.8828 (mtp) cc_final: 0.8535 (mtp) REVERT: D 246 GLU cc_start: 0.8999 (tp30) cc_final: 0.8580 (tp30) REVERT: D 298 MET cc_start: 0.8438 (mpp) cc_final: 0.8177 (mpp) REVERT: D 420 GLN cc_start: 0.8414 (mp10) cc_final: 0.7591 (tp40) REVERT: D 488 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8463 (mm) REVERT: D 617 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7443 (mmtt) REVERT: D 901 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8638 (mm) outliers start: 57 outliers final: 20 residues processed: 296 average time/residue: 0.5043 time to fit residues: 182.9111 Evaluate side-chains 262 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 63 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.156775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098414 restraints weight = 41687.234| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.91 r_work: 0.3284 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29260 Z= 0.128 Angle : 0.573 13.371 39652 Z= 0.277 Chirality : 0.042 0.226 4456 Planarity : 0.003 0.040 5020 Dihedral : 6.336 76.275 3964 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.54 % Allowed : 12.81 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.15), residues: 3524 helix: 0.86 (0.13), residues: 1756 sheet: -1.84 (0.27), residues: 348 loop : 0.03 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 614 TYR 0.009 0.001 TYR C1064 PHE 0.032 0.001 PHE D 300 TRP 0.006 0.001 TRP D 716 HIS 0.003 0.001 HIS D 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (29256) covalent geometry : angle 0.57318 / 0.28 (39644) SS BOND : bond 0.00054 / 0.03 ( 4) SS BOND : angle 0.19185 / 0.10 ( 8) hydrogen bonds : bond 0.03171 / 2.07 ( 1388) hydrogen bonds : angle 4.52649 / 3.24 ( 3708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8750 (m-80) cc_final: 0.8053 (m-80) REVERT: A 173 PHE cc_start: 0.8836 (m-80) cc_final: 0.8519 (m-10) REVERT: A 204 MET cc_start: 0.8834 (mtp) cc_final: 0.8524 (mtp) REVERT: A 298 MET cc_start: 0.8389 (mpp) cc_final: 0.8129 (mpp) REVERT: A 420 GLN cc_start: 0.8354 (mp10) cc_final: 0.7603 (tp40) REVERT: A 488 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 901 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 1064 TYR cc_start: 0.7785 (t80) cc_final: 0.7525 (t80) REVERT: B 19 PHE cc_start: 0.8752 (m-80) cc_final: 0.8057 (m-80) REVERT: B 150 MET cc_start: 0.9213 (ppp) cc_final: 0.8867 (ppp) REVERT: B 154 PHE cc_start: 0.9439 (m-80) cc_final: 0.8863 (m-80) REVERT: B 173 PHE cc_start: 0.8836 (m-80) cc_final: 0.8518 (m-10) REVERT: B 204 MET cc_start: 0.8840 (mtp) cc_final: 0.8532 (mtp) REVERT: B 298 MET cc_start: 0.8389 (mpp) cc_final: 0.8129 (mpp) REVERT: B 420 GLN cc_start: 0.8350 (mp10) cc_final: 0.7599 (tp40) REVERT: B 488 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8456 (mm) REVERT: B 617 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7451 (mmtt) REVERT: B 901 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8661 (mm) REVERT: C 19 PHE cc_start: 0.8751 (m-80) cc_final: 0.8054 (m-80) REVERT: C 173 PHE cc_start: 0.8832 (m-80) cc_final: 0.8516 (m-10) REVERT: C 204 MET cc_start: 0.8833 (mtp) cc_final: 0.8525 (mtp) REVERT: C 298 MET cc_start: 0.8376 (mpp) cc_final: 0.8121 (mpp) REVERT: C 420 GLN cc_start: 0.8364 (mp10) cc_final: 0.7607 (tp40) REVERT: C 488 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (mm) REVERT: C 604 LYS cc_start: 0.9272 (mmmm) cc_final: 0.9048 (mptt) REVERT: C 901 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8649 (mm) REVERT: C 1064 TYR cc_start: 0.7775 (t80) cc_final: 0.7520 (t80) REVERT: D 150 MET cc_start: 0.9216 (ppp) cc_final: 0.8869 (ppp) REVERT: D 154 PHE cc_start: 0.9438 (m-80) cc_final: 0.8861 (m-80) REVERT: D 173 PHE cc_start: 0.8834 (m-80) cc_final: 0.8491 (m-10) REVERT: D 204 MET cc_start: 0.8836 (mtp) cc_final: 0.8528 (mtp) REVERT: D 298 MET cc_start: 0.8386 (mpp) cc_final: 0.8129 (mpp) REVERT: D 420 GLN cc_start: 0.8361 (mp10) cc_final: 0.7610 (tp40) REVERT: D 488 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8453 (mm) REVERT: D 617 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7458 (mmtt) REVERT: D 901 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8665 (mm) outliers start: 48 outliers final: 17 residues processed: 274 average time/residue: 0.5043 time to fit residues: 171.2833 Evaluate side-chains 253 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 10 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 301 optimal weight: 0.9990 chunk 257 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.155957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097375 restraints weight = 40374.659| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.87 r_work: 0.3261 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29260 Z= 0.134 Angle : 0.576 15.724 39652 Z= 0.276 Chirality : 0.042 0.172 4456 Planarity : 0.003 0.040 5020 Dihedral : 6.234 73.809 3964 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.77 % Allowed : 13.32 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.15), residues: 3524 helix: 0.87 (0.13), residues: 1756 sheet: -1.78 (0.27), residues: 348 loop : 0.07 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 614 TYR 0.010 0.001 TYR C1025 PHE 0.022 0.001 PHE A 145 TRP 0.008 0.001 TRP D 235 HIS 0.003 0.001 HIS D 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (29256) covalent geometry : angle 0.57605 / 0.28 (39644) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 0.16123 / 0.09 ( 8) hydrogen bonds : bond 0.03161 / 2.05 ( 1388) hydrogen bonds : angle 4.53776 / 3.25 ( 3708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8798 (m-80) cc_final: 0.8092 (m-80) REVERT: A 173 PHE cc_start: 0.8813 (m-80) cc_final: 0.8503 (m-10) REVERT: A 204 MET cc_start: 0.8752 (mtp) cc_final: 0.8434 (mtp) REVERT: A 420 GLN cc_start: 0.8358 (mp10) cc_final: 0.7620 (tp40) REVERT: A 488 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 617 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7445 (mmtt) REVERT: A 901 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8676 (mm) REVERT: B 19 PHE cc_start: 0.8798 (m-80) cc_final: 0.8092 (m-80) REVERT: B 173 PHE cc_start: 0.8810 (m-80) cc_final: 0.8502 (m-10) REVERT: B 204 MET cc_start: 0.8758 (mtp) cc_final: 0.8442 (mtp) REVERT: B 298 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: B 420 GLN cc_start: 0.8327 (mp10) cc_final: 0.7621 (tp40) REVERT: B 488 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8506 (mm) REVERT: B 617 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7661 (mmtt) REVERT: B 901 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 19 PHE cc_start: 0.8797 (m-80) cc_final: 0.8092 (m-80) REVERT: C 173 PHE cc_start: 0.8807 (m-80) cc_final: 0.8500 (m-10) REVERT: C 204 MET cc_start: 0.8752 (mtp) cc_final: 0.8435 (mtp) REVERT: C 298 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: C 420 GLN cc_start: 0.8371 (mp10) cc_final: 0.7624 (tp40) REVERT: C 488 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8516 (mm) REVERT: C 604 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9044 (mptt) REVERT: C 617 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7440 (mmtt) REVERT: C 901 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8666 (mm) REVERT: C 1064 TYR cc_start: 0.7710 (t80) cc_final: 0.7364 (t80) REVERT: D 19 PHE cc_start: 0.8798 (m-80) cc_final: 0.8096 (m-80) REVERT: D 173 PHE cc_start: 0.8783 (m-80) cc_final: 0.8477 (m-10) REVERT: D 204 MET cc_start: 0.8821 (mtp) cc_final: 0.8500 (mtp) REVERT: D 288 LEU cc_start: 0.8931 (pp) cc_final: 0.8729 (pp) REVERT: D 298 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (mpp) REVERT: D 420 GLN cc_start: 0.8375 (mp10) cc_final: 0.7628 (tp40) REVERT: D 488 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8509 (mm) REVERT: D 617 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7666 (mmtt) REVERT: D 901 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8678 (mm) outliers start: 55 outliers final: 27 residues processed: 283 average time/residue: 0.5059 time to fit residues: 176.7118 Evaluate side-chains 266 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 891 GLU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 193 optimal weight: 30.0000 chunk 61 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 312 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 50.0000 chunk 126 optimal weight: 0.0670 chunk 175 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.157240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099185 restraints weight = 40889.763| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.89 r_work: 0.3290 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 29260 Z= 0.110 Angle : 0.588 19.089 39652 Z= 0.277 Chirality : 0.041 0.227 4456 Planarity : 0.003 0.041 5020 Dihedral : 6.049 71.934 3964 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.71 % Allowed : 13.93 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.15), residues: 3524 helix: 0.93 (0.13), residues: 1756 sheet: -1.71 (0.27), residues: 348 loop : 0.10 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 614 TYR 0.009 0.001 TYR C 938 PHE 0.033 0.001 PHE B 241 TRP 0.005 0.001 TRP D 391 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (29256) covalent geometry : angle 0.58833 / 0.28 (39644) SS BOND : bond 0.00071 / 0.04 ( 4) SS BOND : angle 0.09111 / 0.05 ( 8) hydrogen bonds : bond 0.03035 / 1.97 ( 1388) hydrogen bonds : angle 4.53284 / 3.24 ( 3708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8788 (m-80) cc_final: 0.8111 (m-80) REVERT: A 173 PHE cc_start: 0.8797 (m-80) cc_final: 0.8463 (m-10) REVERT: A 204 MET cc_start: 0.8862 (mtp) cc_final: 0.8566 (mtp) REVERT: A 420 GLN cc_start: 0.8343 (mp10) cc_final: 0.7625 (tp40) REVERT: A 488 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 496 MET cc_start: 0.8400 (mtm) cc_final: 0.8106 (mtm) REVERT: A 617 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7636 (mmtt) REVERT: A 821 MET cc_start: 0.8761 (tpp) cc_final: 0.8533 (tpt) REVERT: A 901 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 1064 TYR cc_start: 0.7663 (t80) cc_final: 0.7400 (t80) REVERT: B 19 PHE cc_start: 0.8790 (m-80) cc_final: 0.8114 (m-80) REVERT: B 154 PHE cc_start: 0.9432 (m-80) cc_final: 0.8804 (m-80) REVERT: B 173 PHE cc_start: 0.8794 (m-80) cc_final: 0.8461 (m-10) REVERT: B 204 MET cc_start: 0.8869 (mtp) cc_final: 0.8575 (mtp) REVERT: B 420 GLN cc_start: 0.8348 (mp10) cc_final: 0.7626 (tp40) REVERT: B 488 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8474 (mm) REVERT: B 496 MET cc_start: 0.8381 (mtm) cc_final: 0.8081 (mtm) REVERT: B 617 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7641 (mmtt) REVERT: B 821 MET cc_start: 0.8704 (tpp) cc_final: 0.8462 (tpt) REVERT: B 901 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8660 (mm) REVERT: C 19 PHE cc_start: 0.8787 (m-80) cc_final: 0.8110 (m-80) REVERT: C 173 PHE cc_start: 0.8792 (m-80) cc_final: 0.8460 (m-10) REVERT: C 204 MET cc_start: 0.8864 (mtp) cc_final: 0.8572 (mtp) REVERT: C 298 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (mpp) REVERT: C 420 GLN cc_start: 0.8347 (mp10) cc_final: 0.7633 (tp40) REVERT: C 488 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8484 (mm) REVERT: C 496 MET cc_start: 0.8395 (mtm) cc_final: 0.8100 (mtm) REVERT: C 617 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7627 (mmtt) REVERT: C 901 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8651 (mm) REVERT: D 19 PHE cc_start: 0.8788 (m-80) cc_final: 0.8112 (m-80) REVERT: D 173 PHE cc_start: 0.8768 (m-80) cc_final: 0.8459 (m-10) REVERT: D 204 MET cc_start: 0.8872 (mtp) cc_final: 0.8576 (mtp) REVERT: D 420 GLN cc_start: 0.8353 (mp10) cc_final: 0.7629 (tp40) REVERT: D 488 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8476 (mm) REVERT: D 496 MET cc_start: 0.8382 (mtm) cc_final: 0.8084 (mtm) REVERT: D 617 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7643 (mmtt) REVERT: D 821 MET cc_start: 0.8743 (tpp) cc_final: 0.8504 (tpt) REVERT: D 901 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8661 (mm) outliers start: 53 outliers final: 17 residues processed: 291 average time/residue: 0.5310 time to fit residues: 189.5835 Evaluate side-chains 261 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 219 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 chunk 305 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.156949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098795 restraints weight = 40590.130| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.89 r_work: 0.3282 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29260 Z= 0.129 Angle : 0.614 16.179 39652 Z= 0.292 Chirality : 0.042 0.228 4456 Planarity : 0.003 0.042 5020 Dihedral : 5.941 69.310 3964 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.42 % Allowed : 14.64 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.15), residues: 3524 helix: 1.00 (0.13), residues: 1732 sheet: -1.66 (0.27), residues: 348 loop : 0.24 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 614 TYR 0.008 0.001 TYR A 938 PHE 0.027 0.001 PHE C 304 TRP 0.006 0.001 TRP C 391 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (29256) covalent geometry : angle 0.61421 / 0.29 (39644) SS BOND : bond 0.00062 / 0.03 ( 4) SS BOND : angle 0.08227 / 0.05 ( 8) hydrogen bonds : bond 0.03150 / 2.06 ( 1388) hydrogen bonds : angle 4.58407 / 3.29 ( 3708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8790 (m-80) cc_final: 0.8112 (m-80) REVERT: A 173 PHE cc_start: 0.8754 (m-80) cc_final: 0.8447 (m-10) REVERT: A 204 MET cc_start: 0.8864 (mtp) cc_final: 0.8567 (mtp) REVERT: A 420 GLN cc_start: 0.8299 (mp10) cc_final: 0.7636 (tp40) REVERT: A 488 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 617 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7620 (mmtt) REVERT: A 901 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 1064 TYR cc_start: 0.7666 (t80) cc_final: 0.7408 (t80) REVERT: B 19 PHE cc_start: 0.8789 (m-80) cc_final: 0.8109 (m-80) REVERT: B 173 PHE cc_start: 0.8751 (m-80) cc_final: 0.8449 (m-10) REVERT: B 204 MET cc_start: 0.8872 (mtp) cc_final: 0.8575 (mtp) REVERT: B 420 GLN cc_start: 0.8304 (mp10) cc_final: 0.7640 (tp40) REVERT: B 488 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8426 (mm) REVERT: B 617 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7439 (mmtt) REVERT: B 901 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8639 (mm) REVERT: C 19 PHE cc_start: 0.8787 (m-80) cc_final: 0.8109 (m-80) REVERT: C 173 PHE cc_start: 0.8751 (m-80) cc_final: 0.8444 (m-10) REVERT: C 204 MET cc_start: 0.8867 (mtp) cc_final: 0.8569 (mtp) REVERT: C 420 GLN cc_start: 0.8350 (mp10) cc_final: 0.7642 (tp40) REVERT: C 488 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8463 (mm) REVERT: C 617 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7615 (mmtt) REVERT: C 901 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8632 (mm) REVERT: D 19 PHE cc_start: 0.8787 (m-80) cc_final: 0.8110 (m-80) REVERT: D 173 PHE cc_start: 0.8749 (m-80) cc_final: 0.8447 (m-10) REVERT: D 204 MET cc_start: 0.8873 (mtp) cc_final: 0.8578 (mtp) REVERT: D 420 GLN cc_start: 0.8361 (mp10) cc_final: 0.7646 (tp40) REVERT: D 488 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8421 (mm) REVERT: D 617 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7439 (mmtt) REVERT: D 901 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8639 (mm) outliers start: 44 outliers final: 25 residues processed: 269 average time/residue: 0.5332 time to fit residues: 176.4450 Evaluate side-chains 267 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 891 GLU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 320 optimal weight: 0.4980 chunk 235 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.157069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099058 restraints weight = 40491.896| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.87 r_work: 0.3282 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29260 Z= 0.127 Angle : 0.612 14.824 39652 Z= 0.295 Chirality : 0.042 0.220 4456 Planarity : 0.003 0.045 5020 Dihedral : 5.850 66.915 3964 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.38 % Allowed : 14.54 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.15), residues: 3524 helix: 0.99 (0.13), residues: 1732 sheet: -1.62 (0.27), residues: 348 loop : 0.29 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 614 TYR 0.008 0.001 TYR A 938 PHE 0.031 0.002 PHE B 118 TRP 0.006 0.001 TRP D 391 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (29256) covalent geometry : angle 0.61202 / 0.29 (39644) SS BOND : bond 0.00063 / 0.03 ( 4) SS BOND : angle 0.07417 / 0.05 ( 8) hydrogen bonds : bond 0.03142 / 2.06 ( 1388) hydrogen bonds : angle 4.60027 / 3.31 ( 3708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8768 (m-80) cc_final: 0.8127 (m-80) REVERT: A 173 PHE cc_start: 0.8797 (m-80) cc_final: 0.8507 (m-10) REVERT: A 204 MET cc_start: 0.8855 (mtp) cc_final: 0.8549 (mtp) REVERT: A 274 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: A 420 GLN cc_start: 0.8315 (mp10) cc_final: 0.7669 (tp40) REVERT: A 488 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8502 (mm) REVERT: A 617 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7615 (mmtt) REVERT: A 901 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8667 (mm) REVERT: A 1064 TYR cc_start: 0.7649 (t80) cc_final: 0.7394 (t80) REVERT: B 19 PHE cc_start: 0.8767 (m-80) cc_final: 0.8129 (m-80) REVERT: B 173 PHE cc_start: 0.8799 (m-80) cc_final: 0.8510 (m-10) REVERT: B 204 MET cc_start: 0.8864 (mtp) cc_final: 0.8561 (mtp) REVERT: B 274 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: B 420 GLN cc_start: 0.8317 (mp10) cc_final: 0.7669 (tp40) REVERT: B 488 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8486 (mm) REVERT: B 617 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7612 (mmtt) REVERT: B 901 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8667 (mm) REVERT: C 19 PHE cc_start: 0.8764 (m-80) cc_final: 0.8122 (m-80) REVERT: C 173 PHE cc_start: 0.8790 (m-80) cc_final: 0.8501 (m-10) REVERT: C 204 MET cc_start: 0.8858 (mtp) cc_final: 0.8555 (mtp) REVERT: C 274 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: C 420 GLN cc_start: 0.8316 (mp10) cc_final: 0.7675 (tp40) REVERT: C 488 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8563 (mm) REVERT: C 617 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7599 (mmtt) REVERT: C 901 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8659 (mm) REVERT: D 19 PHE cc_start: 0.8770 (m-80) cc_final: 0.8137 (m-80) REVERT: D 173 PHE cc_start: 0.8796 (m-80) cc_final: 0.8507 (m-10) REVERT: D 204 MET cc_start: 0.8862 (mtp) cc_final: 0.8560 (mtp) REVERT: D 274 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: D 420 GLN cc_start: 0.8319 (mp10) cc_final: 0.7671 (tp40) REVERT: D 488 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8489 (mm) REVERT: D 617 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7610 (mmtt) REVERT: D 901 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8668 (mm) outliers start: 43 outliers final: 28 residues processed: 266 average time/residue: 0.5294 time to fit residues: 173.9459 Evaluate side-chains 266 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 269 optimal weight: 50.0000 chunk 13 optimal weight: 5.9990 chunk 214 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 286 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 314 optimal weight: 0.0770 chunk 242 optimal weight: 1.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.155768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097327 restraints weight = 41174.158| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.83 r_work: 0.3231 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29260 Z= 0.159 Angle : 0.636 15.075 39652 Z= 0.306 Chirality : 0.043 0.388 4456 Planarity : 0.003 0.053 5020 Dihedral : 5.809 64.412 3964 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.48 % Allowed : 14.93 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.15), residues: 3524 helix: 0.96 (0.13), residues: 1736 sheet: -1.63 (0.27), residues: 348 loop : 0.28 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 614 TYR 0.011 0.001 TYR A1025 PHE 0.048 0.002 PHE C 296 TRP 0.007 0.001 TRP B 391 HIS 0.003 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (29256) covalent geometry : angle 0.63570 / 0.31 (39644) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.12967 / 0.08 ( 8) hydrogen bonds : bond 0.03282 / 2.14 ( 1388) hydrogen bonds : angle 4.63957 / 3.34 ( 3708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9721.97 seconds wall clock time: 166 minutes 25.36 seconds (9985.36 seconds total)