Starting phenix.real_space_refine on Sun Jul 5 16:33:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvi_34128/07_2026/7yvi_34128.cif" } resolution = 3.7 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= -0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18479 2.51 5 N 4774 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28961 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "A" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.01, per 1000 atoms: 0.21 Number of scatterers: 28961 At special positions: 0 Unit cell: (171.38, 147.6, 201.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5579 8.00 N 4774 7.00 C 18479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.02 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 20.5% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.503A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.432A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.702A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.833A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.690A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.348A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.996A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.540A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.902A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.802A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.146A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.831A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.515A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.639A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.780A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.972A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.600A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.188A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.988A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.978A pdb=" N ASP J 31 " --> pdb=" O MET J 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.729A pdb=" N THR J 91 " --> pdb=" O VAL J 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.623A pdb=" N ASP O 31 " --> pdb=" O MET O 28 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER O 32 " --> pdb=" O ILE O 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 28 through 32' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR O 91 " --> pdb=" O VAL O 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.057A pdb=" N ASP K 31 " --> pdb=" O MET K 28 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.543A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.535A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.169A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.556A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.517A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.267A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.570A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.514A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.109A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.990A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.566A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.445A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.030A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.281A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.075A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.339A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.452A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.892A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.566A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.950A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.170A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.170A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.144A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.662A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.873A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.195A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.258A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.981A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.815A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.640A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.571A pdb=" N VAL H 108 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 86 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU H 48 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.571A pdb=" N VAL H 108 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA H 86 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.694A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR J 80 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.480A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR J 59 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.510A pdb=" N THR N 109 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 12 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 86 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.510A pdb=" N THR N 109 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY N 12 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 86 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER N 92 " --> pdb=" O VAL N 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 18 through 22 Processing sheet with id=AF6, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.061A pdb=" N SER O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.863A pdb=" N VAL I 108 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA I 86 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.863A pdb=" N VAL I 108 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA I 86 " --> pdb=" O VAL I 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AG2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.904A pdb=" N MET K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7874 1.33 - 1.47: 10469 1.47 - 1.60: 11131 1.60 - 1.74: 34 1.74 - 1.88: 131 Bond restraints: 29639 Sorted by residual: bond pdb=" CA THR C1066 " pdb=" CB THR C1066 " ideal model delta sigma weight residual 1.534 1.404 0.130 2.33e-02 1.84e+03 3.11e+01 bond pdb=" CB ASN B 907 " pdb=" CG ASN B 907 " ideal model delta sigma weight residual 1.516 1.380 0.136 2.50e-02 1.60e+03 2.97e+01 bond pdb=" CA THR B1066 " pdb=" CB THR B1066 " ideal model delta sigma weight residual 1.534 1.415 0.120 2.33e-02 1.84e+03 2.65e+01 bond pdb=" CB ILE C 714 " pdb=" CG2 ILE C 714 " ideal model delta sigma weight residual 1.521 1.357 0.164 3.30e-02 9.18e+02 2.48e+01 bond pdb=" CB THR A1077 " pdb=" CG2 THR A1077 " ideal model delta sigma weight residual 1.521 1.358 0.163 3.30e-02 9.18e+02 2.43e+01 ... (remaining 29634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 38822 3.79 - 7.58: 1443 7.58 - 11.37: 141 11.37 - 15.17: 33 15.17 - 18.96: 8 Bond angle restraints: 40447 Sorted by residual: angle pdb=" N GLY A 416 " pdb=" CA GLY A 416 " pdb=" C GLY A 416 " ideal model delta sigma weight residual 113.18 96.12 17.06 2.37e+00 1.78e-01 5.18e+01 angle pdb=" CA CYS A 649 " pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " ideal model delta sigma weight residual 114.40 129.17 -14.77 2.30e+00 1.89e-01 4.12e+01 angle pdb=" CB LEU B 878 " pdb=" CG LEU B 878 " pdb=" CD2 LEU B 878 " ideal model delta sigma weight residual 110.70 91.74 18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C PHE C 565 " pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " ideal model delta sigma weight residual 109.79 97.14 12.65 2.05e+00 2.38e-01 3.81e+01 angle pdb=" CA CYS C 538 " pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " ideal model delta sigma weight residual 114.40 128.43 -14.03 2.30e+00 1.89e-01 3.72e+01 ... (remaining 40442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15651 17.69 - 35.38: 1245 35.38 - 53.07: 219 53.07 - 70.76: 44 70.76 - 88.44: 22 Dihedral angle restraints: 17181 sinusoidal: 6249 harmonic: 10932 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.84 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.04 -76.96 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.98 -74.02 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 17178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3526 0.103 - 0.206: 988 0.206 - 0.309: 147 0.309 - 0.412: 21 0.412 - 0.515: 5 Chirality restraints: 4687 Sorted by residual: chirality pdb=" CA CYS A 649 " pdb=" N CYS A 649 " pdb=" C CYS A 649 " pdb=" CB CYS A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CB VAL C1094 " pdb=" CA VAL C1094 " pdb=" CG1 VAL C1094 " pdb=" CG2 VAL C1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CB VAL B1094 " pdb=" CA VAL B1094 " pdb=" CG1 VAL B1094 " pdb=" CG2 VAL B1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 4684 not shown) Planarity restraints: 5188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 67 " -0.074 9.50e-02 1.11e+02 5.93e-02 3.09e+01 pdb=" NE ARG J 67 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG J 67 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG J 67 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG J 67 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 115 " -0.021 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP O 115 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP O 115 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP O 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP O 115 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP O 115 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 115 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 115 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 115 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP O 115 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 374 " 0.049 2.00e-02 2.50e+03 3.68e-02 2.36e+01 pdb=" CG PHE B 374 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE B 374 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 374 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 374 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 374 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 374 " 0.017 2.00e-02 2.50e+03 ... (remaining 5185 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 716 2.60 - 3.18: 26798 3.18 - 3.75: 41826 3.75 - 4.33: 55046 4.33 - 4.90: 94985 Nonbonded interactions: 219371 Sorted by model distance: nonbonded pdb=" OG SER O 7 " pdb=" OG SER O 21 " model vdw 2.028 3.040 nonbonded pdb=" O LYS C 440 " pdb=" OH TYR I 32 " model vdw 2.032 3.040 nonbonded pdb=" OD2 ASP B 737 " pdb=" ND2 ASN A 317 " model vdw 2.036 3.120 nonbonded pdb=" NH1 ARG N 63 " pdb=" O GLY N 79 " model vdw 2.051 3.120 nonbonded pdb=" ND2 ASN A1134 " pdb=" O7 NAG A1308 " model vdw 2.053 3.120 ... (remaining 219366 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' selection = (chain 'B' and resid 27 through 1312) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 26.410 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.026 0.195 29684 Z= 1.064 Angle : 1.697 18.957 40537 Z= 0.928 Chirality : 0.095 0.515 4687 Planarity : 0.009 0.114 5188 Dihedral : 13.238 88.444 10050 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.33 % Favored : 94.05 % Rotamer: Outliers : 1.33 % Allowed : 9.18 % Favored : 89.49 % Cbeta Deviations : 0.06 % 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: -2.56 (0.12), residues: 3717 helix: 0.08 (0.20), residues: 634 sheet: -1.46 (0.14), residues: 987 loop : -2.47 (0.11), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.003 ARG J 67 TYR 0.059 0.005 TYR B 674 PHE 0.080 0.008 PHE B 374 TRP 0.079 0.007 TRP O 115 HIS 0.025 0.005 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.02581 / 1.06 (29639) covalent geometry : angle 1.68472 / 0.92 (40447) SS BOND : bond 0.01308 / 0.89 ( 45) SS BOND : angle 4.56673 / 3.12 ( 90) hydrogen bonds : bond 0.24464 / 16.34 ( 1110) hydrogen bonds : angle 8.83384 / 6.10 ( 3009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TRP cc_start: 0.7039 (m-90) cc_final: 0.6745 (m-90) REVERT: C 191 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8133 (mt-10) REVERT: C 202 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7446 (mmtp) REVERT: C 357 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8354 (tpt-90) REVERT: B 129 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7965 (pttp) REVERT: B 170 TYR cc_start: 0.8236 (t80) cc_final: 0.7851 (t80) REVERT: B 190 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7101 (mtt90) REVERT: B 202 LYS cc_start: 0.7885 (mttp) cc_final: 0.7327 (mppt) REVERT: B 265 TYR cc_start: 0.6796 (p90) cc_final: 0.6338 (p90) REVERT: B 347 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 403 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7742 (ttm-80) REVERT: B 440 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6837 (tmtt) REVERT: B 1138 TYR cc_start: 0.7574 (m-80) cc_final: 0.7260 (m-80) REVERT: A 105 ILE cc_start: 0.7534 (pt) cc_final: 0.6705 (pt) REVERT: A 239 GLN cc_start: 0.7349 (mp10) cc_final: 0.6352 (mp10) REVERT: A 532 ASN cc_start: 0.9112 (t0) cc_final: 0.8782 (t0) REVERT: A 725 GLU cc_start: 0.7935 (tt0) cc_final: 0.7701 (tt0) REVERT: A 1005 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8292 (tp40) REVERT: H 98 THR cc_start: 0.5261 (m) cc_final: 0.4959 (p) REVERT: J 83 MET cc_start: -0.4471 (mmt) cc_final: -0.4675 (mmm) REVERT: N 108 VAL cc_start: 0.8133 (t) cc_final: 0.7402 (t) REVERT: O 22 CYS cc_start: 0.5604 (t) cc_final: 0.4639 (t) REVERT: O 38 ARG cc_start: 0.4172 (ptt180) cc_final: 0.3747 (ttm170) REVERT: O 67 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6348 (mtm-85) REVERT: K 45 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4462 (mm) outliers start: 40 outliers final: 13 residues processed: 292 average time/residue: 0.1902 time to fit residues: 88.2787 Evaluate side-chains 203 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain O residue 104 TYR Chi-restraints excluded: chain K residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 657 ASN C 755 GLN B 188 ASN B 657 ASN B 755 GLN B 762 GLN B1134 ASN A 165 ASN A 234 ASN A 437 ASN A 505 HIS A 540 ASN A 657 ASN A 801 ASN A 965 GLN H 33 ASN H 39 GLN N 39 GLN O 74 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.174636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106351 restraints weight = 48913.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105570 restraints weight = 28386.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104881 restraints weight = 19683.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105489 restraints weight = 19743.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106441 restraints weight = 15874.683| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29684 Z= 0.155 Angle : 0.680 11.494 40537 Z= 0.358 Chirality : 0.047 0.235 4687 Planarity : 0.005 0.058 5188 Dihedral : 5.186 52.705 4072 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.26 % Allowed : 11.88 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3717 helix: 1.29 (0.21), residues: 635 sheet: -0.81 (0.14), residues: 1048 loop : -2.02 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 72 TYR 0.022 0.002 TYR B 200 PHE 0.020 0.002 PHE C 201 TRP 0.025 0.002 TRP B 353 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (29639) covalent geometry : angle 0.67327 / 0.36 (40447) SS BOND : bond 0.00713 / 0.49 ( 45) SS BOND : angle 2.09468 / 1.41 ( 90) hydrogen bonds : bond 0.06296 / 4.08 ( 1110) hydrogen bonds : angle 6.26847 / 4.30 ( 3009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.9015 (t0) cc_final: 0.8648 (t70) REVERT: C 202 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7189 (mmtp) REVERT: C 317 ASN cc_start: 0.8335 (m-40) cc_final: 0.7916 (m-40) REVERT: C 617 CYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6167 (m) REVERT: C 957 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 960 ASN cc_start: 0.8564 (t0) cc_final: 0.8246 (t0) REVERT: C 1005 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8678 (tp40) REVERT: C 1094 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7894 (m) REVERT: B 129 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8015 (pttp) REVERT: B 170 TYR cc_start: 0.8177 (t80) cc_final: 0.7946 (t80) REVERT: B 190 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7361 (mtt90) REVERT: B 202 LYS cc_start: 0.8075 (mttp) cc_final: 0.7835 (mttp) REVERT: B 378 LYS cc_start: 0.7934 (ptpp) cc_final: 0.7698 (ptmt) REVERT: B 403 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7865 (ttm-80) REVERT: B 440 LYS cc_start: 0.7244 (ttpp) cc_final: 0.6795 (tmtt) REVERT: B 460 ASN cc_start: 0.7508 (m-40) cc_final: 0.7092 (m-40) REVERT: B 987 PRO cc_start: 0.7925 (Cg_exo) cc_final: 0.7700 (Cg_endo) REVERT: B 1005 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8335 (tp40) REVERT: B 1017 GLU cc_start: 0.8421 (tp30) cc_final: 0.8005 (tp30) REVERT: B 1094 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8451 (m) REVERT: B 1135 ASN cc_start: 0.8612 (t0) cc_final: 0.8214 (t0) REVERT: A 88 ASP cc_start: 0.8486 (t0) cc_final: 0.8132 (m-30) REVERT: A 105 ILE cc_start: 0.7440 (pt) cc_final: 0.7239 (pt) REVERT: A 239 GLN cc_start: 0.6976 (mp10) cc_final: 0.6724 (mp10) REVERT: A 1005 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8164 (tp40) REVERT: N 71 ASN cc_start: 0.7588 (m-40) cc_final: 0.7374 (m-40) REVERT: O 22 CYS cc_start: 0.4883 (t) cc_final: 0.4239 (t) REVERT: O 67 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6527 (mtm-85) REVERT: O 78 PHE cc_start: 0.7490 (m-10) cc_final: 0.7244 (m-10) REVERT: O 87 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7690 (mpt90) REVERT: O 98 ARG cc_start: 0.7170 (tmm160) cc_final: 0.6753 (tmt170) REVERT: K 34 MET cc_start: 0.6818 (pmm) cc_final: 0.6320 (pmm) outliers start: 68 outliers final: 26 residues processed: 323 average time/residue: 0.1738 time to fit residues: 92.7103 Evaluate side-chains 250 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain I residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 148 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 326 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 121 optimal weight: 40.0000 chunk 235 optimal weight: 8.9990 chunk 245 optimal weight: 0.0040 chunk 368 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 762 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN A1074 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.171564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100328 restraints weight = 48375.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102432 restraints weight = 31564.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102681 restraints weight = 20741.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102980 restraints weight = 18975.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103253 restraints weight = 19529.320| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29684 Z= 0.200 Angle : 0.676 15.109 40537 Z= 0.352 Chirality : 0.047 0.324 4687 Planarity : 0.004 0.045 5188 Dihedral : 4.942 51.047 4065 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 3.09 % Allowed : 13.81 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 3717 helix: 1.61 (0.21), residues: 642 sheet: -0.53 (0.15), residues: 1083 loop : -1.80 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 56 TYR 0.023 0.002 TYR B1067 PHE 0.021 0.002 PHE C 92 TRP 0.017 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (29639) covalent geometry : angle 0.66457 / 0.35 (40447) SS BOND : bond 0.00789 / 0.49 ( 45) SS BOND : angle 2.66685 / 1.74 ( 90) hydrogen bonds : bond 0.06180 / 4.00 ( 1110) hydrogen bonds : angle 5.92489 / 4.08 ( 3009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.8887 (t0) cc_final: 0.8591 (t70) REVERT: C 202 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7678 (mmtp) REVERT: C 405 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.7957 (p0) REVERT: C 617 CYS cc_start: 0.6358 (OUTLIER) cc_final: 0.6020 (m) REVERT: C 960 ASN cc_start: 0.8597 (t0) cc_final: 0.8234 (t0) REVERT: C 1029 MET cc_start: 0.9127 (tpp) cc_final: 0.8639 (ttm) REVERT: B 170 TYR cc_start: 0.8448 (t80) cc_final: 0.8240 (t80) REVERT: B 190 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7565 (mtt90) REVERT: B 202 LYS cc_start: 0.8429 (mttp) cc_final: 0.7789 (mppt) REVERT: B 378 LYS cc_start: 0.8331 (ptpp) cc_final: 0.8113 (ptmt) REVERT: B 399 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8361 (t) REVERT: B 403 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8428 (ttm-80) REVERT: B 440 LYS cc_start: 0.7193 (ttpp) cc_final: 0.6890 (tttm) REVERT: B 460 ASN cc_start: 0.7578 (m-40) cc_final: 0.7237 (m-40) REVERT: B 493 GLN cc_start: 0.8158 (pt0) cc_final: 0.7821 (pt0) REVERT: B 1017 GLU cc_start: 0.8127 (tp30) cc_final: 0.7858 (tm-30) REVERT: B 1096 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9213 (p) REVERT: A 239 GLN cc_start: 0.7905 (mp10) cc_final: 0.7606 (mp10) REVERT: A 957 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 1005 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8258 (tp40) REVERT: A 1096 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9181 (p) REVERT: O 22 CYS cc_start: 0.4700 (t) cc_final: 0.4448 (t) REVERT: O 67 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7209 (mtm-85) REVERT: K 34 MET cc_start: 0.6892 (pmm) cc_final: 0.6641 (pmm) REVERT: K 51 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6606 (mm) outliers start: 93 outliers final: 55 residues processed: 305 average time/residue: 0.1655 time to fit residues: 83.4957 Evaluate side-chains 261 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 18 optimal weight: 30.0000 chunk 317 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 354 optimal weight: 10.0000 chunk 175 optimal weight: 0.0570 chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 281 optimal weight: 0.0050 chunk 189 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN J 82 GLN N 39 GLN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.173460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101114 restraints weight = 48454.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103827 restraints weight = 31664.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105063 restraints weight = 19160.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105140 restraints weight = 17237.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105525 restraints weight = 16795.770| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29684 Z= 0.131 Angle : 0.604 16.827 40537 Z= 0.314 Chirality : 0.045 0.352 4687 Planarity : 0.004 0.051 5188 Dihedral : 4.705 53.411 4062 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 2.93 % Allowed : 15.07 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.82 (0.13), residues: 3717 helix: 2.04 (0.21), residues: 635 sheet: -0.28 (0.15), residues: 1033 loop : -1.59 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 111 TYR 0.022 0.001 TYR N 93 PHE 0.019 0.001 PHE C 201 TRP 0.014 0.001 TRP B 353 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (29639) covalent geometry : angle 0.59272 / 0.31 (40447) SS BOND : bond 0.00436 / 0.31 ( 45) SS BOND : angle 2.51384 / 1.64 ( 90) hydrogen bonds : bond 0.05101 / 3.29 ( 1110) hydrogen bonds : angle 5.56020 / 3.83 ( 3009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 231 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.9003 (t0) cc_final: 0.8772 (t70) REVERT: C 202 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7454 (mmtp) REVERT: C 238 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6651 (p90) REVERT: C 617 CYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6135 (m) REVERT: C 960 ASN cc_start: 0.8536 (t0) cc_final: 0.8125 (t0) REVERT: C 1029 MET cc_start: 0.9082 (tpp) cc_final: 0.8636 (ttm) REVERT: B 190 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7370 (mtt90) REVERT: B 202 LYS cc_start: 0.8269 (mttp) cc_final: 0.7563 (mppt) REVERT: B 298 GLU cc_start: 0.8496 (tt0) cc_final: 0.8217 (tp30) REVERT: B 378 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7871 (ptmt) REVERT: B 399 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8211 (t) REVERT: B 403 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8229 (ttm-80) REVERT: B 440 LYS cc_start: 0.7139 (ttpp) cc_final: 0.6857 (ttpp) REVERT: B 460 ASN cc_start: 0.7621 (m-40) cc_final: 0.7203 (m-40) REVERT: B 493 GLN cc_start: 0.8152 (pt0) cc_final: 0.7832 (pt0) REVERT: B 902 MET cc_start: 0.9102 (tpt) cc_final: 0.8764 (tpt) REVERT: B 964 LYS cc_start: 0.9095 (tptt) cc_final: 0.8839 (tptt) REVERT: B 1017 GLU cc_start: 0.8286 (tp30) cc_final: 0.7954 (tm-30) REVERT: B 1094 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8758 (m) REVERT: B 1096 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9078 (p) REVERT: A 88 ASP cc_start: 0.8252 (t0) cc_final: 0.8017 (m-30) REVERT: A 105 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7508 (mt) REVERT: A 239 GLN cc_start: 0.7438 (mp10) cc_final: 0.7153 (mp10) REVERT: A 957 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 992 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.9074 (mm110) REVERT: A 1096 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (p) REVERT: N 38 TYR cc_start: 0.7657 (m-10) cc_final: 0.7136 (m-10) REVERT: N 48 LEU cc_start: 0.6859 (pp) cc_final: 0.6533 (pp) REVERT: N 56 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7771 (ttm110) REVERT: O 22 CYS cc_start: 0.5016 (t) cc_final: 0.4534 (t) REVERT: O 67 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7105 (mtm-85) REVERT: O 78 PHE cc_start: 0.7408 (m-10) cc_final: 0.7148 (m-10) REVERT: I 49 MET cc_start: 0.6822 (ppp) cc_final: 0.6603 (ppp) REVERT: K 33 TYR cc_start: 0.5171 (m-80) cc_final: 0.4878 (m-80) REVERT: K 34 MET cc_start: 0.6798 (pmm) cc_final: 0.6509 (pmm) REVERT: K 104 TYR cc_start: 0.6849 (m-80) cc_final: 0.6640 (m-80) outliers start: 88 outliers final: 48 residues processed: 304 average time/residue: 0.1770 time to fit residues: 89.5411 Evaluate side-chains 267 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 137 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 363 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 338 optimal weight: 9.9990 chunk 359 optimal weight: 50.0000 chunk 197 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN N 39 GLN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.170889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099462 restraints weight = 48849.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100219 restraints weight = 34904.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100482 restraints weight = 24431.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100839 restraints weight = 21656.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101280 restraints weight = 21508.924| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29684 Z= 0.216 Angle : 0.664 17.015 40537 Z= 0.346 Chirality : 0.047 0.381 4687 Planarity : 0.004 0.047 5188 Dihedral : 4.750 47.849 4058 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 3.96 % Allowed : 15.07 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.13), residues: 3717 helix: 1.79 (0.21), residues: 636 sheet: -0.24 (0.15), residues: 1017 loop : -1.56 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 111 TYR 0.024 0.002 TYR A1067 PHE 0.020 0.002 PHE A 238 TRP 0.014 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (29639) covalent geometry : angle 0.65183 / 0.34 (40447) SS BOND : bond 0.00500 / 0.33 ( 45) SS BOND : angle 2.80667 / 1.89 ( 90) hydrogen bonds : bond 0.05920 / 3.83 ( 1110) hydrogen bonds : angle 5.64166 / 3.89 ( 3009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 209 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7628 (mmtp) REVERT: C 238 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.7036 (p90) REVERT: C 405 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8000 (p0) REVERT: C 578 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8384 (t70) REVERT: C 617 CYS cc_start: 0.6485 (OUTLIER) cc_final: 0.6173 (m) REVERT: C 960 ASN cc_start: 0.8622 (t0) cc_final: 0.8186 (t0) REVERT: C 1029 MET cc_start: 0.9186 (tpp) cc_final: 0.8706 (ttm) REVERT: B 190 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7460 (mtt90) REVERT: B 202 LYS cc_start: 0.8404 (mttp) cc_final: 0.7753 (mppt) REVERT: B 378 LYS cc_start: 0.8290 (ptpp) cc_final: 0.8026 (ptmt) REVERT: B 399 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8328 (t) REVERT: B 403 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8248 (ttm-80) REVERT: B 440 LYS cc_start: 0.7185 (ttpp) cc_final: 0.6771 (tmtt) REVERT: B 460 ASN cc_start: 0.7620 (m-40) cc_final: 0.6991 (m-40) REVERT: B 493 GLN cc_start: 0.8147 (pt0) cc_final: 0.7826 (pt0) REVERT: B 1017 GLU cc_start: 0.8257 (tp30) cc_final: 0.7869 (tm-30) REVERT: B 1094 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8867 (m) REVERT: A 239 GLN cc_start: 0.7869 (mp10) cc_final: 0.7536 (mp10) REVERT: A 957 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 992 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.9084 (mm110) REVERT: A 1005 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8267 (tp40) REVERT: A 1096 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9218 (m) REVERT: N 48 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6496 (tt) REVERT: N 50 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5872 (tp) REVERT: N 56 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7850 (ttm110) REVERT: N 64 PHE cc_start: 0.7937 (m-80) cc_final: 0.7728 (m-80) REVERT: O 22 CYS cc_start: 0.4765 (t) cc_final: 0.4350 (t) REVERT: O 67 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7214 (mtm-85) REVERT: O 78 PHE cc_start: 0.7360 (m-10) cc_final: 0.7076 (m-10) REVERT: K 33 TYR cc_start: 0.5201 (m-80) cc_final: 0.4865 (m-80) REVERT: K 34 MET cc_start: 0.6823 (pmm) cc_final: 0.6491 (pmm) REVERT: K 104 TYR cc_start: 0.6802 (m-80) cc_final: 0.6535 (m-80) outliers start: 119 outliers final: 81 residues processed: 308 average time/residue: 0.1701 time to fit residues: 87.5691 Evaluate side-chains 290 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 198 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 240 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 223 optimal weight: 0.0370 chunk 224 optimal weight: 6.9990 chunk 350 optimal weight: 0.0870 chunk 144 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 overall best weight: 1.0250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN A 965 GLN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN I 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.172852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101480 restraints weight = 48615.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103160 restraints weight = 32195.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103575 restraints weight = 21724.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103816 restraints weight = 19760.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104124 restraints weight = 18949.552| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29684 Z= 0.138 Angle : 0.590 15.360 40537 Z= 0.308 Chirality : 0.045 0.324 4687 Planarity : 0.004 0.053 5188 Dihedral : 4.502 43.696 4058 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.86 % Rotamer: Outliers : 3.39 % Allowed : 16.50 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.60 (0.13), residues: 3717 helix: 2.02 (0.21), residues: 641 sheet: -0.06 (0.16), residues: 1004 loop : -1.41 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 567 TYR 0.023 0.001 TYR N 93 PHE 0.020 0.001 PHE C 201 TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (29639) covalent geometry : angle 0.58040 / 0.30 (40447) SS BOND : bond 0.00453 / 0.32 ( 45) SS BOND : angle 2.33962 / 1.57 ( 90) hydrogen bonds : bond 0.05044 / 3.25 ( 1110) hydrogen bonds : angle 5.37788 / 3.71 ( 3009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 216 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7433 (mttp) REVERT: C 238 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6852 (p90) REVERT: C 405 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8008 (p0) REVERT: C 617 CYS cc_start: 0.6334 (OUTLIER) cc_final: 0.6079 (m) REVERT: C 960 ASN cc_start: 0.8551 (t0) cc_final: 0.8098 (t0) REVERT: C 1029 MET cc_start: 0.9168 (tpp) cc_final: 0.8748 (ttm) REVERT: B 190 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7434 (mtt90) REVERT: B 202 LYS cc_start: 0.8394 (mttp) cc_final: 0.7700 (mppt) REVERT: B 378 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7990 (ptmt) REVERT: B 383 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8093 (p) REVERT: B 399 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 403 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8368 (ttm-80) REVERT: B 440 LYS cc_start: 0.7156 (ttpp) cc_final: 0.6739 (tmtt) REVERT: B 493 GLN cc_start: 0.8172 (pt0) cc_final: 0.7843 (pt0) REVERT: B 902 MET cc_start: 0.9185 (tpt) cc_final: 0.8877 (tpt) REVERT: B 904 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7179 (m-10) REVERT: B 957 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 964 LYS cc_start: 0.9113 (tptt) cc_final: 0.8875 (tptt) REVERT: B 1017 GLU cc_start: 0.8262 (tp30) cc_final: 0.7990 (tm-30) REVERT: B 1094 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8870 (m) REVERT: A 226 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7962 (mt) REVERT: A 239 GLN cc_start: 0.7664 (mp10) cc_final: 0.7207 (mp10) REVERT: A 957 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 992 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9052 (mm110) REVERT: A 1096 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9176 (m) REVERT: N 48 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6287 (tt) REVERT: N 50 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5987 (tp) REVERT: O 22 CYS cc_start: 0.4791 (t) cc_final: 0.4322 (t) REVERT: O 67 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7173 (mtm-85) REVERT: O 78 PHE cc_start: 0.7525 (m-10) cc_final: 0.7228 (m-10) REVERT: K 33 TYR cc_start: 0.5159 (m-80) cc_final: 0.4802 (m-80) REVERT: K 34 MET cc_start: 0.6834 (pmm) cc_final: 0.6486 (pmm) REVERT: K 104 TYR cc_start: 0.6893 (m-80) cc_final: 0.6631 (m-80) outliers start: 102 outliers final: 66 residues processed: 298 average time/residue: 0.1724 time to fit residues: 86.2477 Evaluate side-chains 287 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 208 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 284 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 305 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 260 optimal weight: 0.0770 chunk 230 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 276 optimal weight: 0.5980 chunk 333 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.175190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103285 restraints weight = 48644.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105974 restraints weight = 30882.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106211 restraints weight = 19132.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106506 restraints weight = 18639.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106730 restraints weight = 17823.050| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29684 Z= 0.111 Angle : 0.573 19.418 40537 Z= 0.297 Chirality : 0.044 0.391 4687 Planarity : 0.004 0.050 5188 Dihedral : 4.237 33.316 4058 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.00 % Favored : 94.89 % Rotamer: Outliers : 2.86 % Allowed : 17.13 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.40 (0.14), residues: 3717 helix: 2.27 (0.21), residues: 634 sheet: 0.07 (0.16), residues: 993 loop : -1.30 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 765 TYR 0.022 0.001 TYR N 93 PHE 0.016 0.001 PHE A 238 TRP 0.012 0.001 TRP B 886 HIS 0.004 0.000 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (29639) covalent geometry : angle 0.56155 / 0.29 (40447) SS BOND : bond 0.00441 / 0.29 ( 45) SS BOND : angle 2.51140 / 1.69 ( 90) hydrogen bonds : bond 0.04527 / 2.92 ( 1110) hydrogen bonds : angle 5.13994 / 3.55 ( 3009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 237 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7311 (mttp) REVERT: C 386 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8879 (pttp) REVERT: C 405 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8003 (p0) REVERT: C 960 ASN cc_start: 0.8509 (t0) cc_final: 0.7851 (t0) REVERT: C 1029 MET cc_start: 0.9043 (tpp) cc_final: 0.8629 (ttm) REVERT: B 190 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7359 (mtt90) REVERT: B 191 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7546 (mt-10) REVERT: B 202 LYS cc_start: 0.8282 (mttp) cc_final: 0.7549 (mppt) REVERT: B 378 LYS cc_start: 0.8197 (ptpp) cc_final: 0.7944 (ptmt) REVERT: B 383 SER cc_start: 0.8230 (m) cc_final: 0.7885 (p) REVERT: B 399 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8217 (t) REVERT: B 403 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8126 (ttm-80) REVERT: B 493 GLN cc_start: 0.8162 (pt0) cc_final: 0.7856 (pt0) REVERT: B 780 GLU cc_start: 0.7927 (tt0) cc_final: 0.7717 (tt0) REVERT: B 902 MET cc_start: 0.9202 (tpt) cc_final: 0.8985 (tpt) REVERT: B 1017 GLU cc_start: 0.8285 (tp30) cc_final: 0.7999 (tm-30) REVERT: B 1094 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8856 (m) REVERT: A 105 ILE cc_start: 0.7713 (pt) cc_final: 0.7460 (mt) REVERT: A 200 TYR cc_start: 0.8970 (m-80) cc_final: 0.8764 (m-80) REVERT: A 239 GLN cc_start: 0.7512 (mp10) cc_final: 0.7150 (mp10) REVERT: A 957 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 992 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.9063 (mm110) REVERT: N 48 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6179 (tt) REVERT: N 50 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6271 (tp) REVERT: N 51 TYR cc_start: 0.5084 (p90) cc_final: 0.4737 (p90) REVERT: O 67 ARG cc_start: 0.7524 (mtm180) cc_final: 0.7097 (mtm-85) REVERT: O 78 PHE cc_start: 0.7606 (m-10) cc_final: 0.7310 (m-10) REVERT: K 33 TYR cc_start: 0.5144 (m-80) cc_final: 0.4816 (m-80) REVERT: K 34 MET cc_start: 0.6729 (pmm) cc_final: 0.6447 (pmm) outliers start: 86 outliers final: 59 residues processed: 308 average time/residue: 0.1743 time to fit residues: 90.2991 Evaluate side-chains 272 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 0.1980 chunk 254 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 172 optimal weight: 0.1980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098196 restraints weight = 48855.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100914 restraints weight = 32746.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101273 restraints weight = 21146.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101709 restraints weight = 20701.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101904 restraints weight = 18331.695| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29684 Z= 0.190 Angle : 0.631 17.313 40537 Z= 0.327 Chirality : 0.046 0.347 4687 Planarity : 0.004 0.052 5188 Dihedral : 4.410 33.953 4057 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 2.93 % Allowed : 18.00 % Favored : 79.08 % 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: -0.50 (0.13), residues: 3717 helix: 2.08 (0.21), residues: 629 sheet: -0.01 (0.16), residues: 974 loop : -1.29 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.026 0.001 TYR A1067 PHE 0.027 0.002 PHE B 374 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (29639) covalent geometry : angle 0.61995 / 0.32 (40447) SS BOND : bond 0.00421 / 0.28 ( 45) SS BOND : angle 2.58483 / 1.74 ( 90) hydrogen bonds : bond 0.05510 / 3.57 ( 1110) hydrogen bonds : angle 5.34427 / 3.69 ( 3009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 203 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.9023 (t0) cc_final: 0.8762 (t70) REVERT: C 201 PHE cc_start: 0.7949 (t80) cc_final: 0.7743 (t80) REVERT: C 202 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7592 (mmtp) REVERT: C 386 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8917 (pttp) REVERT: C 405 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8026 (p0) REVERT: C 465 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: C 960 ASN cc_start: 0.8544 (t0) cc_final: 0.7932 (t0) REVERT: C 1029 MET cc_start: 0.9178 (tpp) cc_final: 0.8748 (ttm) REVERT: B 190 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7661 (mtt90) REVERT: B 202 LYS cc_start: 0.8399 (mttp) cc_final: 0.7701 (mppt) REVERT: B 383 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8043 (p) REVERT: B 399 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8290 (t) REVERT: B 403 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: B 460 ASN cc_start: 0.7618 (m-40) cc_final: 0.7159 (m-40) REVERT: B 780 GLU cc_start: 0.7895 (tt0) cc_final: 0.7694 (tt0) REVERT: B 904 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: B 1017 GLU cc_start: 0.8234 (tp30) cc_final: 0.7966 (tm-30) REVERT: B 1094 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9002 (m) REVERT: A 88 ASP cc_start: 0.8078 (m-30) cc_final: 0.7668 (m-30) REVERT: A 105 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (pt) REVERT: A 200 TYR cc_start: 0.8972 (m-80) cc_final: 0.8734 (m-80) REVERT: A 226 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7997 (mt) REVERT: A 239 GLN cc_start: 0.7734 (mp10) cc_final: 0.7241 (mp10) REVERT: A 957 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 992 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.9031 (mm110) REVERT: A 1005 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8227 (tp40) REVERT: N 48 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6250 (tt) REVERT: N 50 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6465 (tp) REVERT: O 67 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7181 (mtm-85) REVERT: O 78 PHE cc_start: 0.7566 (m-10) cc_final: 0.7290 (m-10) REVERT: K 34 MET cc_start: 0.6671 (pmm) cc_final: 0.6442 (pmm) outliers start: 88 outliers final: 68 residues processed: 277 average time/residue: 0.1717 time to fit residues: 80.0540 Evaluate side-chains 279 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 201 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 204 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101935 restraints weight = 48515.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104016 restraints weight = 31610.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104841 restraints weight = 20599.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104822 restraints weight = 18264.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105204 restraints weight = 18476.782| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29684 Z= 0.123 Angle : 0.584 16.064 40537 Z= 0.301 Chirality : 0.044 0.323 4687 Planarity : 0.004 0.051 5188 Dihedral : 4.222 33.264 4057 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 2.93 % Allowed : 17.90 % Favored : 79.17 % 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 (0.14), residues: 3717 helix: 2.32 (0.21), residues: 629 sheet: 0.10 (0.16), residues: 971 loop : -1.19 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.028 0.001 TYR N 93 PHE 0.021 0.001 PHE C 238 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (29639) covalent geometry : angle 0.57378 / 0.30 (40447) SS BOND : bond 0.00382 / 0.27 ( 45) SS BOND : angle 2.35665 / 1.58 ( 90) hydrogen bonds : bond 0.04714 / 3.04 ( 1110) hydrogen bonds : angle 5.13742 / 3.55 ( 3009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 207 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7366 (mttp) REVERT: C 386 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8914 (pttp) REVERT: C 405 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7978 (p0) REVERT: C 960 ASN cc_start: 0.8484 (t0) cc_final: 0.7856 (t0) REVERT: C 1029 MET cc_start: 0.9116 (tpp) cc_final: 0.8679 (ttm) REVERT: B 190 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7496 (mtt90) REVERT: B 202 LYS cc_start: 0.8317 (mttp) cc_final: 0.7651 (mppt) REVERT: B 239 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.5833 (mm110) REVERT: B 269 TYR cc_start: 0.7045 (m-10) cc_final: 0.6692 (m-10) REVERT: B 383 SER cc_start: 0.8282 (m) cc_final: 0.7960 (p) REVERT: B 399 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 403 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8386 (ttm-80) REVERT: B 493 GLN cc_start: 0.7953 (pt0) cc_final: 0.7554 (pt0) REVERT: B 780 GLU cc_start: 0.7865 (tt0) cc_final: 0.7662 (tt0) REVERT: B 902 MET cc_start: 0.9200 (tpt) cc_final: 0.8974 (tpt) REVERT: B 904 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: B 1017 GLU cc_start: 0.8217 (tp30) cc_final: 0.7987 (tm-30) REVERT: B 1094 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8967 (m) REVERT: A 88 ASP cc_start: 0.8124 (m-30) cc_final: 0.7784 (m-30) REVERT: A 105 ILE cc_start: 0.7851 (pt) cc_final: 0.7620 (mt) REVERT: A 200 TYR cc_start: 0.8963 (m-80) cc_final: 0.8762 (m-80) REVERT: A 239 GLN cc_start: 0.7599 (mp10) cc_final: 0.7250 (mp10) REVERT: A 957 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 992 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.9031 (mm110) REVERT: N 48 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6250 (tt) REVERT: N 49 MET cc_start: 0.6838 (mmm) cc_final: 0.5921 (mmp) REVERT: N 50 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6558 (tp) REVERT: O 29 ILE cc_start: 0.7874 (tp) cc_final: 0.7477 (mt) REVERT: O 34 MET cc_start: 0.7334 (mmm) cc_final: 0.6978 (mmm) REVERT: O 67 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7124 (mtm-85) REVERT: K 28 MET cc_start: 0.5545 (ppp) cc_final: 0.5241 (ppp) REVERT: K 34 MET cc_start: 0.6766 (pmm) cc_final: 0.6523 (pmm) outliers start: 88 outliers final: 67 residues processed: 282 average time/residue: 0.1684 time to fit residues: 80.8912 Evaluate side-chains 278 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 202 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 371 optimal weight: 40.0000 chunk 200 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 335 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.172991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100674 restraints weight = 48435.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103536 restraints weight = 31826.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104123 restraints weight = 19759.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104675 restraints weight = 17934.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104857 restraints weight = 17893.997| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29684 Z= 0.130 Angle : 0.583 15.267 40537 Z= 0.301 Chirality : 0.044 0.308 4687 Planarity : 0.004 0.052 5188 Dihedral : 4.164 33.471 4057 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.11 % Favored : 94.78 % Rotamer: Outliers : 2.73 % Allowed : 18.23 % Favored : 79.04 % 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: -0.26 (0.14), residues: 3717 helix: 2.36 (0.21), residues: 632 sheet: 0.13 (0.16), residues: 972 loop : -1.16 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.026 0.001 TYR N 93 PHE 0.033 0.001 PHE O 78 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (29639) covalent geometry : angle 0.57306 / 0.30 (40447) SS BOND : bond 0.00389 / 0.27 ( 45) SS BOND : angle 2.38931 / 1.59 ( 90) hydrogen bonds : bond 0.04714 / 3.04 ( 1110) hydrogen bonds : angle 5.08399 / 3.52 ( 3009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7421 (mttp) REVERT: C 386 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8941 (pttp) REVERT: C 405 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7995 (p0) REVERT: C 960 ASN cc_start: 0.8529 (t0) cc_final: 0.7884 (t0) REVERT: C 1005 GLN cc_start: 0.8612 (tp40) cc_final: 0.8408 (tp40) REVERT: C 1029 MET cc_start: 0.9116 (tpp) cc_final: 0.8677 (ttm) REVERT: B 190 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7483 (mtt90) REVERT: B 202 LYS cc_start: 0.8297 (mttp) cc_final: 0.7648 (mppt) REVERT: B 239 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5818 (mm110) REVERT: B 269 TYR cc_start: 0.7040 (m-10) cc_final: 0.6690 (m-10) REVERT: B 383 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7951 (p) REVERT: B 399 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8268 (t) REVERT: B 403 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8203 (ttm-80) REVERT: B 493 GLN cc_start: 0.8045 (pt0) cc_final: 0.7654 (pt0) REVERT: B 501 TYR cc_start: 0.8231 (m-10) cc_final: 0.7554 (m-80) REVERT: B 902 MET cc_start: 0.9223 (tpt) cc_final: 0.8884 (tpt) REVERT: B 904 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: B 1017 GLU cc_start: 0.8230 (tp30) cc_final: 0.7977 (tm-30) REVERT: B 1094 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8968 (m) REVERT: A 88 ASP cc_start: 0.8008 (m-30) cc_final: 0.7727 (m-30) REVERT: A 239 GLN cc_start: 0.7632 (mp10) cc_final: 0.7301 (mp10) REVERT: A 957 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8273 (tm-30) REVERT: N 44 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7934 (tppt) REVERT: N 48 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6213 (tt) REVERT: N 50 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6789 (tp) REVERT: O 34 MET cc_start: 0.7378 (mmm) cc_final: 0.7110 (mmm) REVERT: O 67 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7161 (mtm-85) REVERT: O 78 PHE cc_start: 0.7479 (m-80) cc_final: 0.7201 (m-80) REVERT: K 34 MET cc_start: 0.6756 (pmm) cc_final: 0.6500 (pmm) outliers start: 82 outliers final: 69 residues processed: 273 average time/residue: 0.1537 time to fit residues: 71.4933 Evaluate side-chains 278 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain K residue 56 TYR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 355 optimal weight: 30.0000 chunk 96 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 chunk 244 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 405 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.175696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102749 restraints weight = 48797.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106394 restraints weight = 30147.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107219 restraints weight = 17907.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106986 restraints weight = 17438.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107306 restraints weight = 17491.563| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29684 Z= 0.105 Angle : 0.563 13.423 40537 Z= 0.289 Chirality : 0.043 0.294 4687 Planarity : 0.004 0.054 5188 Dihedral : 4.011 33.260 4057 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 2.46 % Allowed : 18.56 % Favored : 78.98 % 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: -0.12 (0.14), residues: 3717 helix: 2.49 (0.21), residues: 629 sheet: 0.22 (0.16), residues: 977 loop : -1.06 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 466 TYR 0.025 0.001 TYR N 93 PHE 0.037 0.001 PHE O 78 TRP 0.014 0.001 TRP A 104 HIS 0.004 0.000 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (29639) covalent geometry : angle 0.55498 / 0.29 (40447) SS BOND : bond 0.00353 / 0.26 ( 45) SS BOND : angle 2.04033 / 1.36 ( 90) hydrogen bonds : bond 0.04163 / 2.68 ( 1110) hydrogen bonds : angle 4.92417 / 3.41 ( 3009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5034.78 seconds wall clock time: 87 minutes 49.94 seconds (5269.94 seconds total)