Starting phenix.real_space_refine on Fri Mar 6 10:02:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3m_25663/03_2026/7t3m_25663.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3m_25663/03_2026/7t3m_25663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t3m_25663/03_2026/7t3m_25663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3m_25663/03_2026/7t3m_25663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3m_25663/03_2026/7t3m_25663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3m_25663/03_2026/7t3m_25663.map" } resolution = 3.0 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= 0.012 sd= 1.242 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 132 5.16 5 C 19134 2.51 5 N 4926 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30099 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "C" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "G" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "J" Number of atoms: 832 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 110, 832 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 832 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 110, 832 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 110, 832 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.63, per 1000 atoms: 0.22 Number of scatterers: 30099 At special positions: 0 Unit cell: (154.8, 161.1, 201.6, 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 132 16.00 O 5907 8.00 N 4926 7.00 C 19134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.04 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 282 " " NAG A1206 " - " ASN A 331 " " NAG A1207 " - " ASN A 343 " " NAG A1208 " - " ASN A 603 " " NAG A1209 " - " ASN A 616 " " NAG A1210 " - " ASN A 657 " " NAG A1211 " - " ASN A 709 " " NAG A1212 " - " ASN A 801 " " NAG A1213 " - " ASN A1074 " " NAG A1214 " - " ASN A1098 " " NAG A1215 " - " ASN A1134 " " NAG B 1 " - " ASN A 717 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 234 " " NAG C1205 " - " ASN C 282 " " NAG C1206 " - " ASN C 331 " " NAG C1207 " - " ASN C 343 " " NAG C1208 " - " ASN C 603 " " NAG C1209 " - " ASN C 616 " " NAG C1210 " - " ASN C 657 " " NAG C1211 " - " ASN C 709 " " NAG C1212 " - " ASN C 801 " " NAG C1213 " - " ASN C1074 " " NAG C1214 " - " ASN C1098 " " NAG C1215 " - " ASN C1134 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN G 717 " " NAG G1201 " - " ASN G 61 " " NAG G1202 " - " ASN G 122 " " NAG G1203 " - " ASN G 165 " " NAG G1204 " - " ASN G 234 " " NAG G1205 " - " ASN G 282 " " NAG G1206 " - " ASN G 331 " " NAG G1207 " - " ASN G 343 " " NAG G1208 " - " ASN G 603 " " NAG G1209 " - " ASN G 616 " " NAG G1210 " - " ASN G 657 " " NAG G1211 " - " ASN G 709 " " NAG G1212 " - " ASN G 801 " " NAG G1213 " - " ASN G1074 " " NAG G1214 " - " ASN G1098 " " NAG G1215 " - " ASN G1134 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 63 sheets defined 21.7% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.914A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 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 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 4.602A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1148 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.646A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.675A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 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 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1033 removed outlier: 4.603A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1148 Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.955A pdb=" N LYS D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 3.914A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLU G 773 " --> pdb=" O GLY G 769 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN G 774 " --> pdb=" O ILE G 770 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS G 776 " --> pdb=" O VAL G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 Processing helix chain 'G' and resid 866 through 884 Processing helix chain 'G' and resid 886 through 890 Processing helix chain 'G' and resid 897 through 909 Processing helix chain 'G' and resid 913 through 918 Processing helix chain 'G' and resid 919 through 940 Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 Processing helix chain 'G' and resid 985 through 988 Processing helix chain 'G' and resid 989 through 1033 removed outlier: 4.603A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1116 through 1118 No H-bonds generated for 'chain 'G' and resid 1116 through 1118' Processing helix chain 'G' and resid 1140 through 1148 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.956A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.956A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 27B through 31 removed outlier: 3.898A pdb=" N ASN J 31 " --> pdb=" O ILE J 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 27B through 31 removed outlier: 3.897A pdb=" N ASN K 31 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 27B through 31 removed outlier: 3.898A pdb=" N ASN L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.299A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.674A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.788A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 140 removed outlier: 8.031A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.467A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359 removed outlier: 3.855A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.573A pdb=" N PHE A 565 " --> pdb=" O PHE G 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.503A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.786A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 5.066A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.299A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.675A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.788A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 135 through 140 removed outlier: 8.030A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.467A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 359 removed outlier: 3.856A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.504A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.616A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.768A pdb=" N ILE C 788 " --> pdb=" O ASN G 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 5.066A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.537A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 18 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET D 82 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 29 through 31 removed outlier: 8.299A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS G 207 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LEU G 223 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.675A pdb=" N ASP G 53 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 271 " --> pdb=" O PHE G 55 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.788A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 135 through 140 removed outlier: 8.030A pdb=" N VAL G 159 " --> pdb=" O CYS G 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 311 through 319 removed outlier: 5.468A pdb=" N ILE G 312 " --> pdb=" O THR G 599 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR G 599 " --> pdb=" O ILE G 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN G 314 " --> pdb=" O VAL G 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 597 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 316 " --> pdb=" O VAL G 595 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 356 through 359 removed outlier: 3.855A pdb=" N ASN G 394 " --> pdb=" O GLU G 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'G' and resid 538 through 543 Processing sheet with id=AE8, first strand: chain 'G' and resid 654 through 660 removed outlier: 5.503A pdb=" N THR G 696 " --> pdb=" O VAL G 656 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN G 658 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER G 711 " --> pdb=" O THR G1076 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR G1076 " --> pdb=" O SER G 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 713 " --> pdb=" O ASN G1074 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN G1074 " --> pdb=" O ALA G 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU G1072 " --> pdb=" O PRO G 715 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER G 711 " --> pdb=" O THR G1076 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR G1076 " --> pdb=" O SER G 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 713 " --> pdb=" O ASN G1074 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN G1074 " --> pdb=" O ALA G 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU G1072 " --> pdb=" O PRO G 715 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G1078 " --> pdb=" O PHE G1095 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE G1095 " --> pdb=" O ALA G1078 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G1094 " --> pdb=" O THR G1105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.616A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 1081 through 1083 removed outlier: 5.065A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.536A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.537A pdb=" N THR I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET I 82 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.572A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.572A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG2, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR J 105 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU J 13 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR J 105 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU J 13 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 90 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL J 97 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AG5, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.814A pdb=" N THR K 105 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU K 13 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.814A pdb=" N THR K 105 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU K 13 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER K 90 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL K 97 " --> pdb=" O SER K 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.02 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9552 1.34 - 1.46: 7540 1.46 - 1.58: 13514 1.58 - 1.70: 0 1.70 - 1.82: 171 Bond restraints: 30777 Sorted by residual: bond pdb=" N VAL C 130 " pdb=" CA VAL C 130 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.94e+00 bond pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" N VAL G 130 " pdb=" CA VAL G 130 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.57e+00 bond pdb=" N PHE H 100A" pdb=" CA PHE H 100A" ideal model delta sigma weight residual 1.459 1.492 -0.033 1.41e-02 5.03e+03 5.47e+00 bond pdb=" C TYR H 100B" pdb=" N PRO H 100C" ideal model delta sigma weight residual 1.326 1.357 -0.031 1.44e-02 4.82e+03 4.54e+00 ... (remaining 30772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 41385 2.38 - 4.76: 446 4.76 - 7.14: 37 7.14 - 9.52: 1 9.52 - 11.90: 8 Bond angle restraints: 41877 Sorted by residual: angle pdb=" CB MET I 82C" pdb=" CG MET I 82C" pdb=" SD MET I 82C" ideal model delta sigma weight residual 112.70 122.25 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET H 82C" pdb=" CG MET H 82C" pdb=" SD MET H 82C" ideal model delta sigma weight residual 112.70 122.23 -9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET D 82C" pdb=" CG MET D 82C" pdb=" SD MET D 82C" ideal model delta sigma weight residual 112.70 122.22 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" OG1 THR H 32 " pdb=" CB THR H 32 " pdb=" CG2 THR H 32 " ideal model delta sigma weight residual 109.30 103.30 6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" C ASN A 87 " pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.97e+00 ... (remaining 41872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 17271 17.15 - 34.30: 1328 34.30 - 51.46: 253 51.46 - 68.61: 102 68.61 - 85.76: 39 Dihedral angle restraints: 18993 sinusoidal: 8040 harmonic: 10953 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -35.19 -50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -35.19 -50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS G1082 " pdb=" SG CYS G1082 " pdb=" SG CYS G1126 " pdb=" CB CYS G1126 " ideal model delta sinusoidal sigma weight residual -86.00 -35.20 -50.80 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 18990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3796 0.051 - 0.102: 859 0.102 - 0.153: 226 0.153 - 0.203: 12 0.203 - 0.254: 9 Chirality restraints: 4902 Sorted by residual: chirality pdb=" CA VAL A 130 " pdb=" N VAL A 130 " pdb=" C VAL A 130 " pdb=" CB VAL A 130 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA VAL G 130 " pdb=" N VAL G 130 " pdb=" C VAL G 130 " pdb=" CB VAL G 130 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL C 130 " pdb=" N VAL C 130 " pdb=" C VAL C 130 " pdb=" CB VAL C 130 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4899 not shown) Planarity restraints: 5379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 83 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO D 84 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 84 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 83 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO H 84 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO H 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 84 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 83 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO I 84 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO I 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 84 " 0.036 5.00e-02 4.00e+02 ... (remaining 5376 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1603 2.73 - 3.28: 28428 3.28 - 3.82: 46881 3.82 - 4.36: 54132 4.36 - 4.90: 99294 Nonbonded interactions: 230338 Sorted by model distance: nonbonded pdb=" OG1 THR H 31 " pdb=" CG2 VAL H 34 " model vdw 2.194 3.460 nonbonded pdb=" OG1 THR D 31 " pdb=" CG2 VAL D 34 " model vdw 2.196 3.460 nonbonded pdb=" OG1 THR I 31 " pdb=" CG2 VAL I 34 " model vdw 2.198 3.460 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.244 3.120 nonbonded pdb=" NZ LYS G 811 " pdb=" OG SER G 813 " model vdw 2.245 3.120 ... (remaining 230333 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.400 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.530 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.003 0.042 30873 Z= 0.156 Angle : 0.608 11.903 42120 Z= 0.298 Chirality : 0.047 0.254 4902 Planarity : 0.004 0.066 5331 Dihedral : 13.239 85.761 11814 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.03 % Allowed : 0.70 % Favored : 99.27 % 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: -0.02 (0.14), residues: 3711 helix: 1.44 (0.20), residues: 699 sheet: 0.95 (0.18), residues: 849 loop : -0.94 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 11 TYR 0.011 0.001 TYR G 266 PHE 0.021 0.001 PHE D 100A TRP 0.020 0.001 TRP G 64 HIS 0.002 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00312 (30777) covalent geometry : angle 0.58847 (41877) SS BOND : bond 0.00229 ( 45) SS BOND : angle 0.89451 ( 90) hydrogen bonds : bond 0.22158 ( 1102) hydrogen bonds : angle 8.04511 ( 3144) link_BETA1-4 : bond 0.00266 ( 3) link_BETA1-4 : angle 0.97236 ( 9) link_NAG-ASN : bond 0.00446 ( 48) link_NAG-ASN : angle 2.64719 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 902 MET cc_start: 0.8459 (mmm) cc_final: 0.8242 (mmp) outliers start: 1 outliers final: 1 residues processed: 228 average time/residue: 0.5161 time to fit residues: 143.7798 Evaluate side-chains 145 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1118 ASP 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: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 926 GLN C 409 GLN C 703 ASN C 926 GLN C1002 GLN D 77 GLN G 409 GLN G 926 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.119432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088395 restraints weight = 61257.375| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.83 r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30873 Z= 0.154 Angle : 0.600 11.282 42120 Z= 0.305 Chirality : 0.046 0.228 4902 Planarity : 0.004 0.043 5331 Dihedral : 7.353 56.564 5111 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.91 % Allowed : 6.24 % Favored : 92.85 % 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: 0.14 (0.14), residues: 3711 helix: 1.86 (0.22), residues: 681 sheet: 1.12 (0.18), residues: 837 loop : -0.94 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.014 0.001 TYR G 266 PHE 0.020 0.001 PHE C 168 TRP 0.010 0.001 TRP D 47 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00362 (30777) covalent geometry : angle 0.58046 (41877) SS BOND : bond 0.00426 ( 45) SS BOND : angle 1.54650 ( 90) hydrogen bonds : bond 0.04647 ( 1102) hydrogen bonds : angle 5.71726 ( 3144) link_BETA1-4 : bond 0.00755 ( 3) link_BETA1-4 : angle 1.49241 ( 9) link_NAG-ASN : bond 0.00379 ( 48) link_NAG-ASN : angle 2.40768 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.061 Fit side-chains REVERT: A 318 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7197 (p90) REVERT: A 1002 GLN cc_start: 0.7571 (tt0) cc_final: 0.7219 (pt0) REVERT: D 5 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8470 (mppt) REVERT: D 7 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8103 (m) REVERT: D 75 LYS cc_start: 0.7982 (pmtt) cc_final: 0.7775 (pttm) REVERT: G 153 MET cc_start: 0.4877 (ppp) cc_final: 0.4677 (ppp) REVERT: I 7 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8164 (m) outliers start: 30 outliers final: 12 residues processed: 166 average time/residue: 0.5485 time to fit residues: 110.9334 Evaluate side-chains 147 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 1141 LEU Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 123 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 322 optimal weight: 0.3980 chunk 276 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN G 703 ASN I 77 GLN J 89 GLN K 89 GLN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085690 restraints weight = 61369.342| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.82 r_work: 0.3142 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30873 Z= 0.173 Angle : 0.598 10.994 42120 Z= 0.303 Chirality : 0.046 0.211 4902 Planarity : 0.004 0.043 5331 Dihedral : 7.010 58.882 5109 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.73 % Allowed : 8.87 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3711 helix: 1.83 (0.22), residues: 678 sheet: 0.98 (0.17), residues: 864 loop : -1.06 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1039 TYR 0.014 0.001 TYR L 86 PHE 0.025 0.002 PHE G 906 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00417 (30777) covalent geometry : angle 0.58241 (41877) SS BOND : bond 0.00430 ( 45) SS BOND : angle 1.52844 ( 90) hydrogen bonds : bond 0.04932 ( 1102) hydrogen bonds : angle 5.22623 ( 3144) link_BETA1-4 : bond 0.00154 ( 3) link_BETA1-4 : angle 1.09251 ( 9) link_NAG-ASN : bond 0.00364 ( 48) link_NAG-ASN : angle 2.12550 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 166 CYS cc_start: 0.5616 (m) cc_final: 0.5212 (m) REVERT: A 318 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7471 (p90) REVERT: C 153 MET cc_start: 0.4880 (ppp) cc_final: 0.4670 (ppp) REVERT: D 5 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8692 (mmtm) REVERT: G 153 MET cc_start: 0.5214 (ppp) cc_final: 0.4740 (ppp) REVERT: I 75 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7983 (pttm) outliers start: 57 outliers final: 30 residues processed: 187 average time/residue: 0.5370 time to fit residues: 122.4073 Evaluate side-chains 164 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 233 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 367 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 358 optimal weight: 3.9990 chunk 362 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086169 restraints weight = 61195.899| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.81 r_work: 0.3151 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30873 Z= 0.133 Angle : 0.564 10.682 42120 Z= 0.284 Chirality : 0.045 0.221 4902 Planarity : 0.004 0.043 5331 Dihedral : 6.727 57.657 5109 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.09 % Allowed : 11.44 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3711 helix: 1.88 (0.22), residues: 681 sheet: 1.03 (0.18), residues: 843 loop : -1.04 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 38 TYR 0.014 0.001 TYR G1067 PHE 0.016 0.001 PHE A 906 TRP 0.010 0.001 TRP I 47 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (30777) covalent geometry : angle 0.54868 (41877) SS BOND : bond 0.00371 ( 45) SS BOND : angle 1.49555 ( 90) hydrogen bonds : bond 0.04244 ( 1102) hydrogen bonds : angle 4.97976 ( 3144) link_BETA1-4 : bond 0.00249 ( 3) link_BETA1-4 : angle 0.98906 ( 9) link_NAG-ASN : bond 0.00342 ( 48) link_NAG-ASN : angle 2.00920 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7788 (tp-100) REVERT: A 318 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7450 (p90) REVERT: C 153 MET cc_start: 0.4848 (ppp) cc_final: 0.4302 (ppp) REVERT: C 900 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: D 7 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8221 (m) REVERT: G 153 MET cc_start: 0.5372 (ppp) cc_final: 0.4864 (ppp) REVERT: I 7 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8335 (m) outliers start: 36 outliers final: 26 residues processed: 165 average time/residue: 0.5419 time to fit residues: 109.3901 Evaluate side-chains 163 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 106 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 282 optimal weight: 0.9980 chunk 330 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 351 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN G 703 ASN K 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.117476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086456 restraints weight = 61259.178| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.81 r_work: 0.3157 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30873 Z= 0.118 Angle : 0.544 10.515 42120 Z= 0.274 Chirality : 0.044 0.219 4902 Planarity : 0.004 0.041 5331 Dihedral : 6.547 56.662 5109 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.85 % Allowed : 12.20 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3711 helix: 1.97 (0.22), residues: 678 sheet: 1.06 (0.18), residues: 846 loop : -1.06 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 38 TYR 0.015 0.001 TYR G1067 PHE 0.011 0.001 PHE A 906 TRP 0.009 0.001 TRP I 47 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00278 (30777) covalent geometry : angle 0.53018 (41877) SS BOND : bond 0.00348 ( 45) SS BOND : angle 1.30210 ( 90) hydrogen bonds : bond 0.04001 ( 1102) hydrogen bonds : angle 4.80167 ( 3144) link_BETA1-4 : bond 0.00208 ( 3) link_BETA1-4 : angle 0.95603 ( 9) link_NAG-ASN : bond 0.00340 ( 48) link_NAG-ASN : angle 1.92691 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5844 (mmm) cc_final: 0.5122 (mpp) REVERT: A 208 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8078 (p) REVERT: A 318 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7465 (p90) REVERT: C 153 MET cc_start: 0.4894 (ppp) cc_final: 0.4389 (ppp) REVERT: C 900 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: D 7 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8236 (m) REVERT: G 153 MET cc_start: 0.5415 (ppp) cc_final: 0.4851 (ppp) REVERT: G 376 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8716 (p) REVERT: G 516 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: I 7 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8319 (m) REVERT: I 86 ASP cc_start: 0.7648 (t0) cc_final: 0.7391 (t0) outliers start: 61 outliers final: 38 residues processed: 185 average time/residue: 0.5065 time to fit residues: 115.5636 Evaluate side-chains 179 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 516 GLU Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 263 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 362 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 227 optimal weight: 0.0070 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 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 = 0.3779 r_free = 0.3779 target = 0.117657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086718 restraints weight = 60817.519| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.80 r_work: 0.3163 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30873 Z= 0.115 Angle : 0.546 10.372 42120 Z= 0.275 Chirality : 0.044 0.219 4902 Planarity : 0.004 0.041 5331 Dihedral : 6.452 56.203 5109 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.85 % Allowed : 12.59 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3711 helix: 1.99 (0.22), residues: 681 sheet: 1.06 (0.18), residues: 846 loop : -1.05 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 38 TYR 0.015 0.001 TYR G1067 PHE 0.010 0.001 PHE C1121 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (30777) covalent geometry : angle 0.53213 (41877) SS BOND : bond 0.00406 ( 45) SS BOND : angle 1.35772 ( 90) hydrogen bonds : bond 0.03875 ( 1102) hydrogen bonds : angle 4.71672 ( 3144) link_BETA1-4 : bond 0.00263 ( 3) link_BETA1-4 : angle 0.98973 ( 9) link_NAG-ASN : bond 0.00329 ( 48) link_NAG-ASN : angle 1.87922 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5712 (mmm) cc_final: 0.4986 (mpp) REVERT: A 489 TYR cc_start: 0.6834 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: C 153 MET cc_start: 0.4876 (ppp) cc_final: 0.4409 (ppp) REVERT: C 900 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8508 (mtm) REVERT: D 7 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8224 (m) REVERT: G 153 MET cc_start: 0.5432 (ppp) cc_final: 0.4813 (ppp) REVERT: G 376 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8712 (p) REVERT: G 516 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: I 7 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8347 (m) REVERT: I 86 ASP cc_start: 0.7647 (t0) cc_final: 0.7152 (t0) REVERT: L 83 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6070 (pp20) outliers start: 61 outliers final: 46 residues processed: 190 average time/residue: 0.5069 time to fit residues: 119.8492 Evaluate side-chains 187 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 516 GLU Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 60 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 243 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 751 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085263 restraints weight = 61177.668| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.82 r_work: 0.3134 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30873 Z= 0.154 Angle : 0.576 10.385 42120 Z= 0.292 Chirality : 0.045 0.218 4902 Planarity : 0.004 0.040 5331 Dihedral : 6.549 57.705 5109 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.12 % Allowed : 13.08 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3711 helix: 1.96 (0.22), residues: 678 sheet: 0.93 (0.17), residues: 867 loop : -1.11 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 328 TYR 0.016 0.001 TYR G1067 PHE 0.014 0.001 PHE A 906 TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00373 (30777) covalent geometry : angle 0.56294 (41877) SS BOND : bond 0.00421 ( 45) SS BOND : angle 1.50118 ( 90) hydrogen bonds : bond 0.04313 ( 1102) hydrogen bonds : angle 4.75533 ( 3144) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 1.04576 ( 9) link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 1.88394 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 147 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5682 (mmm) cc_final: 0.4985 (mpp) REVERT: A 318 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7510 (p90) REVERT: A 489 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: C 153 MET cc_start: 0.4834 (ppp) cc_final: 0.4319 (ppp) REVERT: C 318 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7695 (p90) REVERT: C 900 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: D 7 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8267 (m) REVERT: D 75 LYS cc_start: 0.8568 (pttm) cc_final: 0.8338 (pttm) REVERT: D 83 ASP cc_start: 0.7135 (t0) cc_final: 0.6093 (p0) REVERT: G 153 MET cc_start: 0.5440 (ppp) cc_final: 0.4833 (ppp) REVERT: G 173 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7686 (tp-100) REVERT: G 516 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: I 7 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8338 (m) REVERT: I 86 ASP cc_start: 0.7635 (t0) cc_final: 0.7273 (t0) REVERT: L 83 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6030 (pp20) outliers start: 70 outliers final: 46 residues processed: 198 average time/residue: 0.5205 time to fit residues: 126.7719 Evaluate side-chains 193 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 516 GLU Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 364 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 336 optimal weight: 0.0870 chunk 284 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084868 restraints weight = 61494.294| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.80 r_work: 0.3151 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30873 Z= 0.138 Angle : 0.562 10.546 42120 Z= 0.286 Chirality : 0.044 0.222 4902 Planarity : 0.004 0.039 5331 Dihedral : 6.490 57.338 5109 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.18 % Allowed : 13.11 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3711 helix: 1.99 (0.22), residues: 678 sheet: 0.97 (0.18), residues: 846 loop : -1.10 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 38 TYR 0.016 0.001 TYR G1067 PHE 0.010 0.001 PHE G1121 TRP 0.014 0.001 TRP A 64 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00331 (30777) covalent geometry : angle 0.54878 (41877) SS BOND : bond 0.00398 ( 45) SS BOND : angle 1.37680 ( 90) hydrogen bonds : bond 0.04143 ( 1102) hydrogen bonds : angle 4.69442 ( 3144) link_BETA1-4 : bond 0.00181 ( 3) link_BETA1-4 : angle 0.99608 ( 9) link_NAG-ASN : bond 0.00304 ( 48) link_NAG-ASN : angle 1.87098 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 145 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 VAL cc_start: -0.0899 (OUTLIER) cc_final: -0.1112 (t) REVERT: A 318 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7554 (p90) REVERT: A 489 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: A 586 ASP cc_start: 0.8482 (m-30) cc_final: 0.8202 (m-30) REVERT: C 153 MET cc_start: 0.4641 (ppp) cc_final: 0.4030 (ppp) REVERT: C 213 VAL cc_start: -0.0991 (OUTLIER) cc_final: -0.1248 (t) REVERT: C 318 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7725 (p90) REVERT: C 900 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8568 (mtm) REVERT: D 75 LYS cc_start: 0.8587 (pttm) cc_final: 0.8314 (pttm) REVERT: D 83 ASP cc_start: 0.7129 (t0) cc_final: 0.6257 (p0) REVERT: G 153 MET cc_start: 0.5456 (ppp) cc_final: 0.4844 (ppp) REVERT: G 376 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8761 (p) REVERT: G 516 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: H 83 ASP cc_start: 0.6675 (t0) cc_final: 0.5950 (p0) REVERT: I 7 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8339 (m) REVERT: I 83 ASP cc_start: 0.7186 (t0) cc_final: 0.6149 (p0) REVERT: J 81 GLU cc_start: 0.6845 (tp30) cc_final: 0.6585 (tp30) REVERT: K 82 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7494 (p0) REVERT: K 83 GLU cc_start: 0.7275 (mm-30) cc_final: 0.5908 (pp20) REVERT: L 83 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6093 (pp20) outliers start: 72 outliers final: 52 residues processed: 200 average time/residue: 0.4864 time to fit residues: 120.8944 Evaluate side-chains 197 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 135 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 516 GLU Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** H 77 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.114610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083584 restraints weight = 61647.920| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.71 r_work: 0.3111 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30873 Z= 0.213 Angle : 0.642 11.240 42120 Z= 0.327 Chirality : 0.047 0.224 4902 Planarity : 0.004 0.042 5331 Dihedral : 6.806 59.941 5109 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.18 % Allowed : 13.32 % Favored : 84.50 % 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: -0.11 (0.14), residues: 3711 helix: 1.82 (0.22), residues: 687 sheet: 0.82 (0.17), residues: 936 loop : -1.21 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 158 TYR 0.017 0.002 TYR G1067 PHE 0.017 0.002 PHE D 100D TRP 0.019 0.002 TRP A 64 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00518 (30777) covalent geometry : angle 0.62775 (41877) SS BOND : bond 0.00510 ( 45) SS BOND : angle 1.77632 ( 90) hydrogen bonds : bond 0.05015 ( 1102) hydrogen bonds : angle 4.91885 ( 3144) link_BETA1-4 : bond 0.00149 ( 3) link_BETA1-4 : angle 1.08753 ( 9) link_NAG-ASN : bond 0.00308 ( 48) link_NAG-ASN : angle 1.98888 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 147 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.6874 (t80) cc_final: 0.6376 (t80) REVERT: A 213 VAL cc_start: -0.0570 (OUTLIER) cc_final: -0.0794 (t) REVERT: A 318 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7619 (p90) REVERT: A 489 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: C 153 MET cc_start: 0.4856 (ppp) cc_final: 0.4335 (ppp) REVERT: C 318 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7832 (p90) REVERT: C 489 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: C 900 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8693 (mtm) REVERT: G 153 MET cc_start: 0.5630 (ppp) cc_final: 0.5138 (ppp) REVERT: G 213 VAL cc_start: -0.0572 (OUTLIER) cc_final: -0.0865 (t) REVERT: G 516 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: H 83 ASP cc_start: 0.6793 (t0) cc_final: 0.5929 (p0) REVERT: I 83 ASP cc_start: 0.7186 (t0) cc_final: 0.6093 (p0) REVERT: K 82 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7543 (p0) REVERT: K 83 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6018 (pp20) REVERT: L 83 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6120 (pp20) outliers start: 72 outliers final: 48 residues processed: 201 average time/residue: 0.4923 time to fit residues: 123.5334 Evaluate side-chains 196 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 516 GLU Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 99 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 346 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 978 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084406 restraints weight = 61270.964| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.70 r_work: 0.3133 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30873 Z= 0.162 Angle : 0.600 12.237 42120 Z= 0.304 Chirality : 0.045 0.235 4902 Planarity : 0.004 0.040 5331 Dihedral : 6.651 59.175 5109 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.88 % Allowed : 14.05 % Favored : 84.08 % 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: -0.11 (0.14), residues: 3711 helix: 1.85 (0.22), residues: 681 sheet: 0.83 (0.17), residues: 918 loop : -1.21 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 38 TYR 0.016 0.001 TYR G1067 PHE 0.012 0.001 PHE G 906 TRP 0.013 0.001 TRP C 64 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00389 (30777) covalent geometry : angle 0.58637 (41877) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.51444 ( 90) hydrogen bonds : bond 0.04456 ( 1102) hydrogen bonds : angle 4.78799 ( 3144) link_BETA1-4 : bond 0.00177 ( 3) link_BETA1-4 : angle 1.02800 ( 9) link_NAG-ASN : bond 0.00303 ( 48) link_NAG-ASN : angle 1.95693 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 VAL cc_start: -0.0499 (OUTLIER) cc_final: -0.0718 (t) REVERT: A 318 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7641 (p90) REVERT: A 489 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: C 153 MET cc_start: 0.4909 (ppp) cc_final: 0.4439 (ppp) REVERT: C 318 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7856 (p90) REVERT: C 489 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: C 900 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (mtm) REVERT: D 83 ASP cc_start: 0.7085 (t0) cc_final: 0.6214 (p0) REVERT: G 153 MET cc_start: 0.5672 (ppp) cc_final: 0.5111 (ppp) REVERT: G 213 VAL cc_start: -0.0600 (OUTLIER) cc_final: -0.0878 (t) REVERT: H 83 ASP cc_start: 0.6747 (t0) cc_final: 0.5902 (p0) REVERT: I 75 LYS cc_start: 0.8388 (pmtt) cc_final: 0.8083 (ttpt) REVERT: I 83 ASP cc_start: 0.7168 (t0) cc_final: 0.6201 (p0) REVERT: L 83 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6126 (pp20) outliers start: 62 outliers final: 45 residues processed: 189 average time/residue: 0.4832 time to fit residues: 113.8950 Evaluate side-chains 188 residues out of total 3303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 262 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 202 optimal weight: 0.2980 chunk 266 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 336 optimal weight: 0.0020 chunk 369 optimal weight: 0.6980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085466 restraints weight = 61479.638| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.80 r_work: 0.3156 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30873 Z= 0.104 Angle : 0.565 11.366 42120 Z= 0.286 Chirality : 0.044 0.231 4902 Planarity : 0.004 0.038 5331 Dihedral : 6.433 56.464 5109 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.36 % Allowed : 14.53 % Favored : 84.11 % 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: -0.07 (0.14), residues: 3711 helix: 1.98 (0.22), residues: 681 sheet: 0.89 (0.18), residues: 846 loop : -1.15 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.015 0.001 TYR G1067 PHE 0.030 0.001 PHE G 157 TRP 0.011 0.001 TRP C 64 HIS 0.001 0.000 HIS G1088 Details of bonding type rmsd covalent geometry : bond 0.00228 (30777) covalent geometry : angle 0.55194 (41877) SS BOND : bond 0.00380 ( 45) SS BOND : angle 1.32341 ( 90) hydrogen bonds : bond 0.03798 ( 1102) hydrogen bonds : angle 4.62722 ( 3144) link_BETA1-4 : bond 0.00224 ( 3) link_BETA1-4 : angle 0.95840 ( 9) link_NAG-ASN : bond 0.00335 ( 48) link_NAG-ASN : angle 1.90914 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8645.64 seconds wall clock time: 148 minutes 12.40 seconds (8892.40 seconds total)