Starting phenix.real_space_refine on Fri Mar 6 06:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rk6_24493/03_2026/7rk6_24493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rk6_24493/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rk6_24493/03_2026/7rk6_24493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rk6_24493/03_2026/7rk6_24493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rk6_24493/03_2026/7rk6_24493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rk6_24493/03_2026/7rk6_24493.map" } 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-5986/lib/python3.9/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: 161 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: 161 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: 161 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: 161 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: 6.03, 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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: 6.13 Time building geometry restraints manager: 3.18 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: 1480 33.57 - 50.35: 310 50.35 - 67.14: 56 67.14 - 83.92: 24 Dihedral angle restraints: 17324 sinusoidal: 6916 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 17321 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: 1.350 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: 0.040 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.270 Find NCS groups from input model: 0.590 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: 0.000 Load rotamer database and sin/cos tables:9.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 13.959 83.925 10584 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 covalent geometry : bond 0.00546 (29256) covalent geometry : angle 0.63103 (39644) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.11422 ( 8) hydrogen bonds : bond 0.16069 ( 1388) hydrogen bonds : angle 6.32582 ( 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 : 0.758 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: 0.5293 time to fit residues: 177.0393 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 : 1.166 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 406 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.156952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098326 restraints weight = 41128.030| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.90 r_work: 0.3298 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1036 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= 0.123 Angle : 0.563 8.152 39652 Z= 0.283 Chirality : 0.042 0.140 4456 Planarity : 0.004 0.042 5020 Dihedral : 7.550 88.347 3972 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.90 % Allowed : 6.95 % Favored : 92.15 % 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: 0.58 (0.13), residues: 1756 sheet: -2.18 (0.28), residues: 348 loop : -0.09 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 614 TYR 0.017 0.001 TYR B 268 PHE 0.020 0.002 PHE A 296 TRP 0.008 0.001 TRP D 391 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00262 (29256) covalent geometry : angle 0.56272 (39644) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.07101 ( 8) hydrogen bonds : bond 0.03829 ( 1388) hydrogen bonds : angle 4.87526 ( 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 307 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9380 (m-80) cc_final: 0.8847 (m-80) REVERT: A 204 MET cc_start: 0.8791 (mtp) cc_final: 0.8550 (mtp) REVERT: A 268 TYR cc_start: 0.8568 (t80) cc_final: 0.8356 (t80) REVERT: A 298 MET cc_start: 0.8480 (mpp) cc_final: 0.8195 (mpp) REVERT: A 420 GLN cc_start: 0.8393 (mp10) cc_final: 0.7419 (tp-100) REVERT: A 814 VAL cc_start: 0.7754 (m) cc_final: 0.6890 (t) REVERT: A 901 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 154 PHE cc_start: 0.9380 (m-80) cc_final: 0.8847 (m-80) REVERT: B 268 TYR cc_start: 0.8570 (t80) cc_final: 0.8356 (t80) REVERT: B 298 MET cc_start: 0.8477 (mpp) cc_final: 0.8192 (mpp) REVERT: B 420 GLN cc_start: 0.8386 (mp10) cc_final: 0.7420 (tp-100) REVERT: B 814 VAL cc_start: 0.7755 (m) cc_final: 0.6882 (t) REVERT: B 901 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8563 (mm) REVERT: C 154 PHE cc_start: 0.9379 (m-80) cc_final: 0.8844 (m-80) REVERT: C 204 MET cc_start: 0.8793 (mtp) cc_final: 0.8550 (mtp) REVERT: C 268 TYR cc_start: 0.8572 (t80) cc_final: 0.8357 (t80) REVERT: C 298 MET cc_start: 0.8475 (mpp) cc_final: 0.8190 (mpp) REVERT: C 420 GLN cc_start: 0.8389 (mp10) cc_final: 0.7414 (tp-100) REVERT: C 814 VAL cc_start: 0.7761 (m) cc_final: 0.6893 (t) REVERT: C 901 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8563 (mm) REVERT: D 154 PHE cc_start: 0.9380 (m-80) cc_final: 0.8847 (m-80) REVERT: D 204 MET cc_start: 0.8792 (mtp) cc_final: 0.8548 (mtp) REVERT: D 268 TYR cc_start: 0.8567 (t80) cc_final: 0.8355 (t80) REVERT: D 298 MET cc_start: 0.8486 (mpp) cc_final: 0.8199 (mpp) REVERT: D 420 GLN cc_start: 0.8392 (mp10) cc_final: 0.7418 (tp-100) REVERT: D 814 VAL cc_start: 0.7758 (m) cc_final: 0.6891 (t) REVERT: D 901 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8557 (mm) outliers start: 28 outliers final: 8 residues processed: 291 average time/residue: 0.5060 time to fit residues: 179.1052 Evaluate side-chains 255 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 243 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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: 0.0980 chunk 186 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 311 optimal weight: 0.1980 chunk 235 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 317 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 894 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.157114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098524 restraints weight = 41437.424| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.93 r_work: 0.3296 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1305 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= 0.116 Angle : 0.543 7.638 39652 Z= 0.270 Chirality : 0.041 0.134 4456 Planarity : 0.003 0.041 5020 Dihedral : 7.149 86.481 3972 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.00 % Allowed : 9.17 % Favored : 89.83 % 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: 0.04 (0.15), residues: 3524 helix: 0.67 (0.13), residues: 1744 sheet: -2.02 (0.28), residues: 348 loop : -0.05 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 382 TYR 0.011 0.001 TYR D 268 PHE 0.022 0.001 PHE B 296 TRP 0.007 0.001 TRP C 716 HIS 0.003 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00260 (29256) covalent geometry : angle 0.54315 (39644) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.08807 ( 8) hydrogen bonds : bond 0.03484 ( 1388) hydrogen bonds : angle 4.70438 ( 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 300 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9408 (m-80) cc_final: 0.8815 (m-80) REVERT: A 204 MET cc_start: 0.8824 (mtp) cc_final: 0.8572 (mtp) REVERT: A 268 TYR cc_start: 0.8445 (t80) cc_final: 0.8229 (t80) REVERT: A 298 MET cc_start: 0.8361 (mpp) cc_final: 0.8080 (mpp) REVERT: A 420 GLN cc_start: 0.8359 (mp10) cc_final: 0.7564 (tp40) REVERT: A 901 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8546 (mm) REVERT: B 154 PHE cc_start: 0.9408 (m-80) cc_final: 0.8814 (m-80) REVERT: B 268 TYR cc_start: 0.8451 (t80) cc_final: 0.8232 (t80) REVERT: B 298 MET cc_start: 0.8360 (mpp) cc_final: 0.8080 (mpp) REVERT: B 420 GLN cc_start: 0.8363 (mp10) cc_final: 0.7567 (tp40) REVERT: B 901 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 154 PHE cc_start: 0.9408 (m-80) cc_final: 0.8813 (m-80) REVERT: C 204 MET cc_start: 0.8826 (mtp) cc_final: 0.8573 (mtp) REVERT: C 268 TYR cc_start: 0.8445 (t80) cc_final: 0.8226 (t80) REVERT: C 298 MET cc_start: 0.8355 (mpp) cc_final: 0.8077 (mpp) REVERT: C 420 GLN cc_start: 0.8361 (mp10) cc_final: 0.7568 (tp40) REVERT: C 901 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8550 (mm) REVERT: D 154 PHE cc_start: 0.9408 (m-80) cc_final: 0.8814 (m-80) REVERT: D 204 MET cc_start: 0.8824 (mtp) cc_final: 0.8570 (mtp) REVERT: D 268 TYR cc_start: 0.8437 (t80) cc_final: 0.8225 (t80) REVERT: D 298 MET cc_start: 0.8355 (mpp) cc_final: 0.8077 (mpp) REVERT: D 420 GLN cc_start: 0.8362 (mp10) cc_final: 0.7565 (tp40) REVERT: D 901 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8547 (mm) outliers start: 31 outliers final: 15 residues processed: 284 average time/residue: 0.4882 time to fit residues: 170.0486 Evaluate side-chains 258 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 572 ILE 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 572 ILE 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: 0.4980 chunk 27 optimal weight: 0.5980 chunk 244 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 296 optimal weight: 0.0040 chunk 53 optimal weight: 1.9990 chunk 345 optimal weight: 5.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.157740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099458 restraints weight = 41566.982| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.90 r_work: 0.3308 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29260 Z= 0.108 Angle : 0.538 8.076 39652 Z= 0.265 Chirality : 0.041 0.133 4456 Planarity : 0.003 0.045 5020 Dihedral : 6.832 85.918 3972 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.42 % Allowed : 10.78 % Favored : 87.81 % 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: 0.17 (0.15), residues: 3524 helix: 0.77 (0.13), residues: 1764 sheet: -1.89 (0.27), residues: 348 loop : 0.00 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 614 TYR 0.010 0.001 TYR A 268 PHE 0.025 0.001 PHE A 241 TRP 0.006 0.001 TRP C 716 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00239 (29256) covalent geometry : angle 0.53761 (39644) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.07407 ( 8) hydrogen bonds : bond 0.03295 ( 1388) hydrogen bonds : angle 4.56214 ( 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 298 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9399 (m-80) cc_final: 0.8833 (m-80) REVERT: A 173 PHE cc_start: 0.8777 (m-80) cc_final: 0.8548 (m-10) REVERT: A 204 MET cc_start: 0.8809 (mtp) cc_final: 0.8557 (mtp) REVERT: A 298 MET cc_start: 0.8385 (mpp) cc_final: 0.8120 (mpp) REVERT: A 300 PHE cc_start: 0.8570 (t80) cc_final: 0.8353 (t80) REVERT: A 420 GLN cc_start: 0.8356 (mp10) cc_final: 0.7517 (tp40) REVERT: A 488 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8444 (mm) REVERT: A 901 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8611 (mm) REVERT: A 1064 TYR cc_start: 0.7749 (t80) cc_final: 0.7402 (t80) REVERT: B 154 PHE cc_start: 0.9401 (m-80) cc_final: 0.8833 (m-80) REVERT: B 173 PHE cc_start: 0.8776 (m-80) cc_final: 0.8547 (m-10) REVERT: B 298 MET cc_start: 0.8377 (mpp) cc_final: 0.8113 (mpp) REVERT: B 420 GLN cc_start: 0.8353 (mp10) cc_final: 0.7517 (tp40) REVERT: B 488 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 901 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8574 (mm) REVERT: B 1064 TYR cc_start: 0.7750 (t80) cc_final: 0.7397 (t80) REVERT: C 154 PHE cc_start: 0.9400 (m-80) cc_final: 0.8828 (m-80) REVERT: C 173 PHE cc_start: 0.8778 (m-80) cc_final: 0.8549 (m-10) REVERT: C 204 MET cc_start: 0.8811 (mtp) cc_final: 0.8558 (mtp) REVERT: C 298 MET cc_start: 0.8380 (mpp) cc_final: 0.8118 (mpp) REVERT: C 300 PHE cc_start: 0.8579 (t80) cc_final: 0.8360 (t80) REVERT: C 420 GLN cc_start: 0.8343 (mp10) cc_final: 0.7514 (tp40) REVERT: C 488 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (mm) REVERT: C 901 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8575 (mm) REVERT: C 1064 TYR cc_start: 0.7751 (t80) cc_final: 0.7501 (t80) REVERT: D 154 PHE cc_start: 0.9400 (m-80) cc_final: 0.8834 (m-80) REVERT: D 173 PHE cc_start: 0.8776 (m-80) cc_final: 0.8546 (m-10) REVERT: D 204 MET cc_start: 0.8806 (mtp) cc_final: 0.8554 (mtp) REVERT: D 298 MET cc_start: 0.8377 (mpp) cc_final: 0.8113 (mpp) REVERT: D 300 PHE cc_start: 0.8574 (t80) cc_final: 0.8358 (t80) REVERT: D 420 GLN cc_start: 0.8350 (mp10) cc_final: 0.7502 (tp40) REVERT: D 488 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8430 (mm) REVERT: D 901 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8613 (mm) REVERT: D 1064 TYR cc_start: 0.7753 (t80) cc_final: 0.7399 (t80) outliers start: 44 outliers final: 12 residues processed: 282 average time/residue: 0.5316 time to fit residues: 181.1615 Evaluate side-chains 252 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 572 ILE 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 488 LEU Chi-restraints excluded: chain B residue 572 ILE 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 488 LEU Chi-restraints excluded: chain C residue 572 ILE 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 488 LEU Chi-restraints excluded: chain D residue 572 ILE 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: 2.9990 chunk 306 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 224 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.154476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095024 restraints weight = 40911.787| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.89 r_work: 0.3225 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 29260 Z= 0.225 Angle : 0.613 15.351 39652 Z= 0.300 Chirality : 0.044 0.251 4456 Planarity : 0.004 0.044 5020 Dihedral : 6.730 85.591 3972 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.93 % Allowed : 12.07 % Favored : 86.00 % 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: 0.01 (0.15), residues: 3524 helix: 0.71 (0.13), residues: 1784 sheet: -1.95 (0.28), residues: 348 loop : -0.20 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.019 0.001 TYR B1025 PHE 0.026 0.002 PHE B 300 TRP 0.008 0.001 TRP D 716 HIS 0.006 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00530 (29256) covalent geometry : angle 0.61298 (39644) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.35283 ( 8) hydrogen bonds : bond 0.03564 ( 1388) hydrogen bonds : angle 4.60946 ( 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 304 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8737 (m-80) cc_final: 0.8036 (m-80) REVERT: A 173 PHE cc_start: 0.8861 (m-80) cc_final: 0.8577 (m-10) REVERT: A 204 MET cc_start: 0.8823 (mtp) cc_final: 0.8560 (mtp) REVERT: A 246 GLU cc_start: 0.8976 (tp30) cc_final: 0.8526 (tp30) REVERT: A 298 MET cc_start: 0.8428 (mpp) cc_final: 0.8165 (mpp) REVERT: A 307 PHE cc_start: 0.8710 (m-10) cc_final: 0.8426 (m-10) REVERT: A 420 GLN cc_start: 0.8430 (mp10) cc_final: 0.7603 (tp40) REVERT: A 488 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8562 (mm) REVERT: A 901 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8623 (mm) REVERT: A 913 LEU cc_start: 0.8676 (tp) cc_final: 0.8473 (tt) REVERT: B 19 PHE cc_start: 0.8755 (m-80) cc_final: 0.8054 (m-80) REVERT: B 173 PHE cc_start: 0.8861 (m-80) cc_final: 0.8578 (m-10) REVERT: B 246 GLU cc_start: 0.8983 (tp30) cc_final: 0.8527 (tp30) REVERT: B 298 MET cc_start: 0.8426 (mpp) cc_final: 0.8153 (mpp) REVERT: B 420 GLN cc_start: 0.8382 (mp10) cc_final: 0.7608 (tp40) REVERT: B 488 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 901 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8655 (mm) REVERT: B 913 LEU cc_start: 0.8675 (tp) cc_final: 0.8474 (tt) REVERT: C 19 PHE cc_start: 0.8748 (m-80) cc_final: 0.8047 (m-80) REVERT: C 173 PHE cc_start: 0.8859 (m-80) cc_final: 0.8578 (m-10) REVERT: C 204 MET cc_start: 0.8823 (mtp) cc_final: 0.8552 (mtp) REVERT: C 246 GLU cc_start: 0.8977 (tp30) cc_final: 0.8531 (tp30) REVERT: C 298 MET cc_start: 0.8421 (mpp) cc_final: 0.8159 (mpp) REVERT: C 420 GLN cc_start: 0.8428 (mp10) cc_final: 0.7607 (tp40) REVERT: C 488 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8557 (mm) REVERT: C 901 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8653 (mm) REVERT: C 913 LEU cc_start: 0.8679 (tp) cc_final: 0.8478 (tt) REVERT: D 19 PHE cc_start: 0.8739 (m-80) cc_final: 0.8040 (m-80) REVERT: D 150 MET cc_start: 0.9216 (ppp) cc_final: 0.8896 (pp-130) REVERT: D 154 PHE cc_start: 0.9420 (m-80) cc_final: 0.8930 (m-80) REVERT: D 173 PHE cc_start: 0.8860 (m-80) cc_final: 0.8577 (m-10) REVERT: D 204 MET cc_start: 0.8821 (mtp) cc_final: 0.8558 (mtp) REVERT: D 298 MET cc_start: 0.8427 (mpp) cc_final: 0.8160 (mpp) REVERT: D 307 PHE cc_start: 0.8706 (m-10) cc_final: 0.8424 (m-10) REVERT: D 420 GLN cc_start: 0.8414 (mp10) cc_final: 0.7619 (tp40) REVERT: D 488 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8559 (mm) REVERT: D 901 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8654 (mm) REVERT: D 913 LEU cc_start: 0.8676 (tp) cc_final: 0.8474 (tt) outliers start: 60 outliers final: 28 residues processed: 288 average time/residue: 0.5167 time to fit residues: 180.4388 Evaluate side-chains 264 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 524 MET Chi-restraints excluded: chain A residue 596 VAL 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 405 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 596 VAL 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 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 524 MET Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 753 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 405 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 596 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 63 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 111 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 299 optimal weight: 0.9980 chunk 326 optimal weight: 2.9990 chunk 307 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.156930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098659 restraints weight = 41556.720| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.91 r_work: 0.3287 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29260 Z= 0.115 Angle : 0.573 14.099 39652 Z= 0.279 Chirality : 0.042 0.148 4456 Planarity : 0.003 0.044 5020 Dihedral : 6.620 85.243 3972 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.51 % Allowed : 13.29 % Favored : 85.20 % 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: 0.21 (0.15), residues: 3524 helix: 0.82 (0.13), residues: 1756 sheet: -1.86 (0.27), residues: 348 loop : 0.00 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 382 TYR 0.010 0.001 TYR A 938 PHE 0.034 0.002 PHE D 300 TRP 0.007 0.001 TRP B 235 HIS 0.003 0.001 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00260 (29256) covalent geometry : angle 0.57259 (39644) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.21305 ( 8) hydrogen bonds : bond 0.03263 ( 1388) hydrogen bonds : angle 4.54797 ( 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 285 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8743 (m-80) cc_final: 0.8011 (m-80) REVERT: A 173 PHE cc_start: 0.8850 (m-80) cc_final: 0.8537 (m-10) REVERT: A 204 MET cc_start: 0.8834 (mtp) cc_final: 0.8529 (mtp) REVERT: A 298 MET cc_start: 0.8432 (mpp) cc_final: 0.8180 (mpp) REVERT: A 420 GLN cc_start: 0.8377 (mp10) cc_final: 0.7600 (tp40) REVERT: A 488 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 901 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8616 (mm) REVERT: B 19 PHE cc_start: 0.8745 (m-80) cc_final: 0.8013 (m-80) REVERT: B 173 PHE cc_start: 0.8850 (m-80) cc_final: 0.8538 (m-10) REVERT: B 298 MET cc_start: 0.8435 (mpp) cc_final: 0.8174 (mpp) REVERT: B 420 GLN cc_start: 0.8376 (mp10) cc_final: 0.7604 (tp40) REVERT: B 488 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 617 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7614 (mmtt) REVERT: B 901 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8614 (mm) REVERT: C 19 PHE cc_start: 0.8744 (m-80) cc_final: 0.8013 (m-80) REVERT: C 173 PHE cc_start: 0.8847 (m-80) cc_final: 0.8535 (m-10) REVERT: C 204 MET cc_start: 0.8830 (mtp) cc_final: 0.8525 (mtp) REVERT: C 298 MET cc_start: 0.8426 (mpp) cc_final: 0.8178 (mpp) REVERT: C 420 GLN cc_start: 0.8379 (mp10) cc_final: 0.7601 (tp40) REVERT: C 488 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8471 (mm) REVERT: C 901 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8644 (mm) REVERT: D 19 PHE cc_start: 0.8744 (m-80) cc_final: 0.8014 (m-80) REVERT: D 150 MET cc_start: 0.9213 (ppp) cc_final: 0.8868 (pp-130) REVERT: D 154 PHE cc_start: 0.9419 (m-80) cc_final: 0.8916 (m-80) REVERT: D 173 PHE cc_start: 0.8847 (m-80) cc_final: 0.8535 (m-10) REVERT: D 204 MET cc_start: 0.8831 (mtp) cc_final: 0.8525 (mtp) REVERT: D 298 MET cc_start: 0.8431 (mpp) cc_final: 0.8163 (mpp) REVERT: D 420 GLN cc_start: 0.8382 (mp10) cc_final: 0.7610 (tp40) REVERT: D 488 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8475 (mm) REVERT: D 617 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7611 (mmtt) REVERT: D 901 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8616 (mm) outliers start: 47 outliers final: 16 residues processed: 274 average time/residue: 0.4783 time to fit residues: 161.8163 Evaluate side-chains 250 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 891 GLU 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 891 GLU 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 891 GLU 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 891 GLU 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: 7.9990 chunk 171 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 291 optimal weight: 0.0980 chunk 276 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.154969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096011 restraints weight = 41027.401| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.88 r_work: 0.3244 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29260 Z= 0.185 Angle : 0.597 15.864 39652 Z= 0.289 Chirality : 0.044 0.249 4456 Planarity : 0.003 0.041 5020 Dihedral : 6.568 84.537 3972 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.67 % Allowed : 13.51 % Favored : 84.81 % 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: 0.04 (0.14), residues: 3524 helix: 0.70 (0.13), residues: 1784 sheet: -1.94 (0.27), residues: 348 loop : -0.13 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 614 TYR 0.014 0.001 TYR A1025 PHE 0.032 0.002 PHE D 300 TRP 0.006 0.001 TRP B 716 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00438 (29256) covalent geometry : angle 0.59674 (39644) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.28627 ( 8) hydrogen bonds : bond 0.03399 ( 1388) hydrogen bonds : angle 4.63979 ( 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 289 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8795 (m-80) cc_final: 0.8087 (m-80) REVERT: A 173 PHE cc_start: 0.8842 (m-80) cc_final: 0.8522 (m-10) REVERT: A 204 MET cc_start: 0.8850 (mtp) cc_final: 0.8537 (mtp) REVERT: A 246 GLU cc_start: 0.8958 (tp30) cc_final: 0.8592 (tp30) REVERT: A 298 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: A 420 GLN cc_start: 0.8312 (mp10) cc_final: 0.7617 (tp40) REVERT: A 488 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8551 (mm) REVERT: A 901 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 913 LEU cc_start: 0.8606 (tp) cc_final: 0.8345 (tt) REVERT: B 19 PHE cc_start: 0.8790 (m-80) cc_final: 0.8083 (m-80) REVERT: B 173 PHE cc_start: 0.8841 (m-80) cc_final: 0.8498 (m-10) REVERT: B 298 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: B 420 GLN cc_start: 0.8315 (mp10) cc_final: 0.7621 (tp40) REVERT: B 488 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8542 (mm) REVERT: B 617 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7481 (mmtt) REVERT: B 901 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8669 (mm) REVERT: B 913 LEU cc_start: 0.8609 (tp) cc_final: 0.8348 (tt) REVERT: C 19 PHE cc_start: 0.8791 (m-80) cc_final: 0.8084 (m-80) REVERT: C 173 PHE cc_start: 0.8839 (m-80) cc_final: 0.8521 (m-10) REVERT: C 204 MET cc_start: 0.8846 (mtp) cc_final: 0.8534 (mtp) REVERT: C 298 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: C 420 GLN cc_start: 0.8322 (mp10) cc_final: 0.7623 (tp40) REVERT: C 488 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 604 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8996 (mptt) REVERT: C 913 LEU cc_start: 0.8611 (tp) cc_final: 0.8349 (tt) REVERT: D 19 PHE cc_start: 0.8793 (m-80) cc_final: 0.8087 (m-80) REVERT: D 173 PHE cc_start: 0.8840 (m-80) cc_final: 0.8525 (m-10) REVERT: D 204 MET cc_start: 0.8848 (mtp) cc_final: 0.8538 (mtp) REVERT: D 298 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8152 (mpp) REVERT: D 420 GLN cc_start: 0.8313 (mp10) cc_final: 0.7622 (tp40) REVERT: D 488 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8548 (mm) REVERT: D 617 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7486 (mmtt) REVERT: D 901 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8666 (mm) REVERT: D 913 LEU cc_start: 0.8606 (tp) cc_final: 0.8349 (tt) outliers start: 52 outliers final: 23 residues processed: 269 average time/residue: 0.5053 time to fit residues: 165.7124 Evaluate side-chains 263 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET 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 944 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 524 MET 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 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 596 VAL Chi-restraints excluded: chain C residue 944 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 901 LEU Chi-restraints excluded: chain D residue 944 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: 8.9990 chunk 61 optimal weight: 0.8980 chunk 243 optimal weight: 0.0170 chunk 312 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 50.0000 chunk 126 optimal weight: 0.0170 chunk 175 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.157620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099495 restraints weight = 41032.525| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.91 r_work: 0.3298 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29260 Z= 0.103 Angle : 0.575 13.835 39652 Z= 0.276 Chirality : 0.042 0.196 4456 Planarity : 0.003 0.044 5020 Dihedral : 6.332 84.779 3972 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.51 % Allowed : 14.70 % Favored : 83.78 % 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: 0.32 (0.15), residues: 3524 helix: 0.92 (0.13), residues: 1756 sheet: -1.76 (0.27), residues: 348 loop : 0.03 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 196 TYR 0.010 0.001 TYR D 938 PHE 0.026 0.001 PHE A 153 TRP 0.007 0.001 TRP B 789 HIS 0.003 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00226 (29256) covalent geometry : angle 0.57542 (39644) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.10264 ( 8) hydrogen bonds : bond 0.03136 ( 1388) hydrogen bonds : angle 4.53370 ( 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 305 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8783 (m-80) cc_final: 0.8104 (m-80) REVERT: A 173 PHE cc_start: 0.8802 (m-80) cc_final: 0.8461 (m-10) REVERT: A 204 MET cc_start: 0.8855 (mtp) cc_final: 0.8563 (mtp) REVERT: A 246 GLU cc_start: 0.8991 (tp30) cc_final: 0.8759 (tp30) REVERT: A 298 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8094 (mpp) REVERT: A 420 GLN cc_start: 0.8340 (mp10) cc_final: 0.7620 (tp40) REVERT: A 488 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 617 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7594 (mmtt) REVERT: B 173 PHE cc_start: 0.8772 (m-80) cc_final: 0.8458 (m-10) REVERT: B 246 GLU cc_start: 0.8997 (tp30) cc_final: 0.8774 (tp30) REVERT: B 298 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: B 420 GLN cc_start: 0.8338 (mp10) cc_final: 0.7618 (tp40) REVERT: B 488 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8451 (mm) REVERT: B 617 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7591 (mmtt) REVERT: C 19 PHE cc_start: 0.8779 (m-80) cc_final: 0.8101 (m-80) REVERT: C 173 PHE cc_start: 0.8798 (m-80) cc_final: 0.8458 (m-10) REVERT: C 204 MET cc_start: 0.8855 (mtp) cc_final: 0.8564 (mtp) REVERT: C 246 GLU cc_start: 0.8990 (tp30) cc_final: 0.8762 (tp30) REVERT: C 420 GLN cc_start: 0.8299 (mp10) cc_final: 0.7624 (tp40) REVERT: C 488 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (mm) REVERT: C 604 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8979 (mptt) REVERT: C 1064 TYR cc_start: 0.7678 (t80) cc_final: 0.7344 (t80) REVERT: D 19 PHE cc_start: 0.8772 (m-80) cc_final: 0.8093 (m-80) REVERT: D 173 PHE cc_start: 0.8802 (m-80) cc_final: 0.8464 (m-10) REVERT: D 204 MET cc_start: 0.8858 (mtp) cc_final: 0.8570 (mtp) REVERT: D 298 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8155 (mpp) REVERT: D 420 GLN cc_start: 0.8345 (mp10) cc_final: 0.7624 (tp40) REVERT: D 488 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8451 (mm) REVERT: D 617 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7590 (mmtt) outliers start: 47 outliers final: 17 residues processed: 292 average time/residue: 0.5070 time to fit residues: 180.5980 Evaluate side-chains 264 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET 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 969 MET Chi-restraints excluded: chain B residue 298 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 945 THR 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 891 GLU Chi-restraints excluded: chain C residue 945 THR 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 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 891 GLU 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: 2.9990 chunk 36 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 chunk 305 optimal weight: 0.8980 chunk 246 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 325 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098467 restraints weight = 40551.237| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.87 r_work: 0.3277 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29260 Z= 0.131 Angle : 0.610 17.084 39652 Z= 0.287 Chirality : 0.042 0.191 4456 Planarity : 0.003 0.044 5020 Dihedral : 6.227 83.950 3972 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.64 % Allowed : 14.99 % Favored : 83.37 % 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: -1.74 (0.27), residues: 348 loop : 0.06 (0.17), residues: 1420 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 0.029 0.001 PHE B 300 TRP 0.005 0.001 TRP D 716 HIS 0.003 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00313 (29256) covalent geometry : angle 0.61006 (39644) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.09549 ( 8) hydrogen bonds : bond 0.03184 ( 1388) hydrogen bonds : angle 4.60738 ( 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 295 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8793 (m-80) cc_final: 0.8115 (m-80) REVERT: A 173 PHE cc_start: 0.8828 (m-80) cc_final: 0.8519 (m-10) REVERT: A 204 MET cc_start: 0.8867 (mtp) cc_final: 0.8573 (mtp) REVERT: A 246 GLU cc_start: 0.9110 (tp30) cc_final: 0.8734 (tp30) REVERT: A 298 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: A 420 GLN cc_start: 0.8319 (mp10) cc_final: 0.7642 (tp40) REVERT: A 488 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 617 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7619 (mmtt) REVERT: B 19 PHE cc_start: 0.8795 (m-80) cc_final: 0.8121 (m-80) REVERT: B 173 PHE cc_start: 0.8807 (m-80) cc_final: 0.8490 (m-10) REVERT: B 246 GLU cc_start: 0.9121 (tp30) cc_final: 0.8752 (tp30) REVERT: B 298 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8097 (mpp) REVERT: B 420 GLN cc_start: 0.8327 (mp10) cc_final: 0.7641 (tp40) REVERT: B 488 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8503 (mm) REVERT: B 617 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7621 (mmtt) REVERT: C 19 PHE cc_start: 0.8789 (m-80) cc_final: 0.8112 (m-80) REVERT: C 173 PHE cc_start: 0.8822 (m-80) cc_final: 0.8515 (m-10) REVERT: C 204 MET cc_start: 0.8866 (mtp) cc_final: 0.8574 (mtp) REVERT: C 246 GLU cc_start: 0.9105 (tp30) cc_final: 0.8728 (tp30) REVERT: C 420 GLN cc_start: 0.8324 (mp10) cc_final: 0.7647 (tp40) REVERT: C 488 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8521 (mm) REVERT: C 604 LYS cc_start: 0.9311 (mmmm) cc_final: 0.8984 (mptt) REVERT: C 617 LYS cc_start: 0.7905 (mmtm) cc_final: 0.7611 (mmtt) REVERT: D 19 PHE cc_start: 0.8787 (m-80) cc_final: 0.8114 (m-80) REVERT: D 173 PHE cc_start: 0.8825 (m-80) cc_final: 0.8518 (m-10) REVERT: D 204 MET cc_start: 0.8866 (mtp) cc_final: 0.8575 (mtp) REVERT: D 246 GLU cc_start: 0.9158 (tp30) cc_final: 0.8798 (tp30) REVERT: D 298 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8094 (mpp) REVERT: D 420 GLN cc_start: 0.8331 (mp10) cc_final: 0.7643 (tp40) REVERT: D 488 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8508 (mm) REVERT: D 617 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7620 (mmtt) outliers start: 51 outliers final: 20 residues processed: 279 average time/residue: 0.4726 time to fit residues: 162.5271 Evaluate side-chains 267 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET 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 944 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 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 944 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 891 GLU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 944 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 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 891 GLU 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: 0.8980 chunk 235 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 177 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.157164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099216 restraints weight = 40636.243| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.89 r_work: 0.3293 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29260 Z= 0.120 Angle : 0.610 18.174 39652 Z= 0.288 Chirality : 0.042 0.148 4456 Planarity : 0.003 0.044 5020 Dihedral : 6.158 83.357 3972 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.09 % Allowed : 15.86 % Favored : 83.04 % 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: 0.36 (0.15), residues: 3524 helix: 0.92 (0.13), residues: 1756 sheet: -1.76 (0.27), residues: 348 loop : 0.09 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 382 TYR 0.009 0.001 TYR D 938 PHE 0.045 0.002 PHE B 296 TRP 0.005 0.001 TRP B 391 HIS 0.004 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00277 (29256) covalent geometry : angle 0.60956 (39644) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.08794 ( 8) hydrogen bonds : bond 0.03214 ( 1388) hydrogen bonds : angle 4.60089 ( 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 273 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8766 (m-80) cc_final: 0.8127 (m-80) REVERT: A 173 PHE cc_start: 0.8799 (m-80) cc_final: 0.8487 (m-10) REVERT: A 204 MET cc_start: 0.8864 (mtp) cc_final: 0.8571 (mtp) REVERT: A 246 GLU cc_start: 0.9064 (tp30) cc_final: 0.8716 (tp30) REVERT: A 420 GLN cc_start: 0.8303 (mp10) cc_final: 0.7645 (tp40) REVERT: A 488 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 496 MET cc_start: 0.8405 (mtm) cc_final: 0.8163 (mtm) REVERT: A 617 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7608 (mmtt) REVERT: B 19 PHE cc_start: 0.8775 (m-80) cc_final: 0.8145 (m-80) REVERT: B 173 PHE cc_start: 0.8807 (m-80) cc_final: 0.8538 (m-10) REVERT: B 246 GLU cc_start: 0.9065 (tp30) cc_final: 0.8725 (tp30) REVERT: B 274 MET cc_start: 0.7980 (mmm) cc_final: 0.7718 (mmm) REVERT: B 420 GLN cc_start: 0.8313 (mp10) cc_final: 0.7647 (tp40) REVERT: B 488 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8464 (mm) REVERT: B 496 MET cc_start: 0.8382 (mtm) cc_final: 0.8135 (mtm) REVERT: B 617 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7612 (mmtt) REVERT: C 19 PHE cc_start: 0.8762 (m-80) cc_final: 0.8123 (m-80) REVERT: C 173 PHE cc_start: 0.8792 (m-80) cc_final: 0.8482 (m-10) REVERT: C 204 MET cc_start: 0.8865 (mtp) cc_final: 0.8573 (mtp) REVERT: C 246 GLU cc_start: 0.9060 (tp30) cc_final: 0.8715 (tp30) REVERT: C 420 GLN cc_start: 0.8317 (mp10) cc_final: 0.7653 (tp40) REVERT: C 488 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8473 (mm) REVERT: C 496 MET cc_start: 0.8390 (mtm) cc_final: 0.8141 (mtm) REVERT: C 617 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7604 (mmtt) REVERT: D 19 PHE cc_start: 0.8766 (m-80) cc_final: 0.8135 (m-80) REVERT: D 173 PHE cc_start: 0.8809 (m-80) cc_final: 0.8538 (m-10) REVERT: D 204 MET cc_start: 0.8896 (mtp) cc_final: 0.8615 (mtp) REVERT: D 246 GLU cc_start: 0.9138 (tp30) cc_final: 0.8799 (tp30) REVERT: D 420 GLN cc_start: 0.8325 (mp10) cc_final: 0.7650 (tp40) REVERT: D 488 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (mm) REVERT: D 496 MET cc_start: 0.8383 (mtm) cc_final: 0.8134 (mtm) REVERT: D 617 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7611 (mmtt) outliers start: 34 outliers final: 25 residues processed: 261 average time/residue: 0.5012 time to fit residues: 160.7158 Evaluate side-chains 268 residues out of total 3108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 941 ASP Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 969 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 941 ASP Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 969 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 891 GLU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 969 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 891 GLU 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: 10.0000 chunk 214 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.154468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095536 restraints weight = 39960.240| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.84 r_work: 0.3222 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29260 Z= 0.218 Angle : 0.663 17.270 39652 Z= 0.320 Chirality : 0.044 0.172 4456 Planarity : 0.004 0.042 5020 Dihedral : 6.210 82.201 3972 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.29 % Allowed : 16.06 % Favored : 82.66 % 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: 0.09 (0.14), residues: 3524 helix: 0.70 (0.13), residues: 1788 sheet: -1.80 (0.27), residues: 352 loop : -0.07 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 382 TYR 0.015 0.001 TYR A1025 PHE 0.049 0.002 PHE D 296 TRP 0.009 0.001 TRP A 716 HIS 0.005 0.001 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00515 (29256) covalent geometry : angle 0.66313 (39644) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.29189 ( 8) hydrogen bonds : bond 0.03584 ( 1388) hydrogen bonds : angle 4.76491 ( 3708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9531.10 seconds wall clock time: 162 minutes 50.80 seconds (9770.80 seconds total)