Starting phenix.real_space_refine on Thu Mar 5 20:03:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t67_25711/03_2026/7t67_25711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t67_25711/03_2026/7t67_25711.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t67_25711/03_2026/7t67_25711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t67_25711/03_2026/7t67_25711.map" model { file = "/net/cci-nas-00/data/ceres_data/7t67_25711/03_2026/7t67_25711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t67_25711/03_2026/7t67_25711.cif" } 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= -0.005 sd= 0.174 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 111 5.16 5 C 15771 2.51 5 N 4044 2.21 5 O 4827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s 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: 24753 Number of models: 1 Model: "" Number of chains: 9 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: "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: "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: "D" 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: "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: 5.59, per 1000 atoms: 0.23 Number of scatterers: 24753 At special positions: 0 Unit cell: (157.5, 145.8, 171.9, 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 111 16.00 O 4827 8.00 N 4044 7.00 C 15771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.03 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=2.03 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 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=2.04 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 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 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 603 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG C1210 " - " ASN C 801 " " NAG C1211 " - " ASN C1074 " " NAG C1212 " - " ASN C1098 " " NAG C1213 " - " ASN C1134 " " NAG C1214 " - " ASN C 343 " " NAG C1215 " - " ASN C 331 " " NAG D 1 " - " ASN C 717 " " NAG E 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 603 " " NAG G1207 " - " ASN G 616 " " NAG G1208 " - " ASN G 657 " " NAG G1209 " - " ASN G 709 " " NAG G1210 " - " ASN G 801 " " NAG G1211 " - " ASN G1074 " " NAG G1212 " - " ASN G1098 " " NAG G1213 " - " ASN G1134 " " NAG G1214 " - " ASN G 343 " " NAG G1215 " - " ASN G 331 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 47 sheets defined 25.6% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.959A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.588A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.882A pdb=" N ALA A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.734A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.679A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.508A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.501A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.727A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.445A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for '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: 4.268A 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 1033 removed outlier: 4.918A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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 removed outlier: 3.920A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) 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 371 removed outlier: 4.038A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.898A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.874A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (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 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.705A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.587A 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 891 removed outlier: 3.770A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.028A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.505A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.636A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (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: 4.513A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (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 removed outlier: 3.715A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (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 371 Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.530A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 408 removed outlier: 4.242A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 737 through 744 Processing helix chain 'G' and resid 746 through 754 removed outlier: 3.502A pdb=" N SER G 750 " --> pdb=" O SER G 746 " (cutoff:3.500A) Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.625A pdb=" N GLU G 773 " --> pdb=" O GLY G 769 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN G 774 " --> pdb=" O ILE G 770 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS G 776 " --> pdb=" O VAL G 772 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G 778 " --> pdb=" O GLN G 774 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 removed outlier: 3.572A pdb=" N ASN G 824 " --> pdb=" O ASP G 820 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS G 825 " --> pdb=" O LEU G 821 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL G 826 " --> pdb=" O LEU G 822 " (cutoff:3.500A) Processing helix chain 'G' and resid 866 through 885 removed outlier: 3.683A pdb=" N GLY G 885 " --> pdb=" O THR G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 891 removed outlier: 3.894A pdb=" N ALA G 890 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 909 removed outlier: 3.844A pdb=" N ILE G 909 " --> pdb=" O ARG G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.978A pdb=" N TYR G 917 " --> pdb=" O GLN G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 940 Processing helix chain 'G' and resid 945 through 965 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 removed outlier: 3.540A pdb=" N LEU G 984 " --> pdb=" O ILE G 980 " (cutoff:3.500A) Processing helix chain 'G' and resid 985 through 1034 removed outlier: 4.336A pdb=" N GLU G 990 " --> pdb=" O PRO G 986 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLN G 992 " --> pdb=" O GLU G 988 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU G1034 " --> pdb=" O SER G1030 " (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 removed outlier: 4.210A pdb=" N GLU G1144 " --> pdb=" O PRO G1140 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G1148 " --> pdb=" O GLU G1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.770A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.501A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.532A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.913A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.657A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 removed outlier: 5.395A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 565 " --> pdb=" O PHE G 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.639A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.153A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.835A pdb=" N ALA A 701 " --> pdb=" O ILE G 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.481A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.481A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.564A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.945A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.537A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.000A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.000A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.768A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.601A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.192A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.904A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.510A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.599A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.246A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.151A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.535A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 787 through 790 removed outlier: 3.536A pdb=" N ASN G 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 5.136A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 28 through 30 removed outlier: 7.401A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR G 63 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 93 " --> pdb=" O TYR G 266 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR G 208 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU G 191 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS G 206 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR G 204 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS G 195 " --> pdb=" O LYS G 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS G 202 " --> pdb=" O LYS G 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N HIS G 207 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N LEU G 223 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.643A pdb=" N ASP G 53 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.652A pdb=" N LEU G 84 " --> pdb=" O PHE G 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.652A pdb=" N LEU G 84 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE G 119 " --> pdb=" O TRP G 104 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU G 132 " --> pdb=" O CYS G 166 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS G 166 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLN G 134 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN G 164 " --> pdb=" O GLN G 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 311 through 319 removed outlier: 6.902A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 325 through 328 Processing sheet with id=AE4, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.540A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN G 394 " --> pdb=" O GLU G 516 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU G 516 " --> pdb=" O ASN G 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL G 433 " --> pdb=" O LYS G 378 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS G 378 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.998A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (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 654 through 660 removed outlier: 6.286A pdb=" N GLU G 654 " --> pdb=" O ALA G 694 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N THR G 696 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N VAL G 656 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.729A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G1050 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.729A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR G1076 " --> pdb=" O SER G1097 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA G1078 " --> pdb=" O PHE G1095 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE G1095 " --> pdb=" O ALA G1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 5.540A pdb=" N VAL G1122 " --> pdb=" O PHE G1089 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE G1089 " --> pdb=" O VAL G1122 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY G1124 " --> pdb=" O ALA G1087 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7857 1.34 - 1.47: 6330 1.47 - 1.59: 10974 1.59 - 1.72: 0 1.72 - 1.84: 141 Bond restraints: 25302 Sorted by residual: bond pdb=" N VAL G 433 " pdb=" CA VAL G 433 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.03e+01 bond pdb=" N VAL G 90 " pdb=" CA VAL G 90 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.01e+00 bond pdb=" N LEU C 461 " pdb=" CA LEU C 461 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.40e+00 bond pdb=" N VAL C 615 " pdb=" CA VAL C 615 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.36e+00 ... (remaining 25297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 33848 2.56 - 5.12: 519 5.12 - 7.67: 39 7.67 - 10.23: 5 10.23 - 12.79: 2 Bond angle restraints: 34413 Sorted by residual: angle pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" C ASN A 616 " ideal model delta sigma weight residual 111.71 107.21 4.50 1.15e+00 7.56e-01 1.53e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 125.02 131.90 -6.88 1.76e+00 3.23e-01 1.53e+01 angle pdb=" N ILE G 231 " pdb=" CA ILE G 231 " pdb=" C ILE G 231 " ideal model delta sigma weight residual 110.42 114.17 -3.75 9.60e-01 1.09e+00 1.53e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 angle pdb=" CB LYS A 129 " pdb=" CG LYS A 129 " pdb=" CD LYS A 129 " ideal model delta sigma weight residual 111.30 120.04 -8.74 2.30e+00 1.89e-01 1.45e+01 ... (remaining 34408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14477 17.93 - 35.85: 955 35.85 - 53.78: 229 53.78 - 71.71: 59 71.71 - 89.63: 30 Dihedral angle restraints: 15750 sinusoidal: 6801 harmonic: 8949 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 -16.39 -69.61 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.53 65.47 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 153.85 -60.85 1 1.00e+01 1.00e-02 4.92e+01 ... (remaining 15747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3381 0.068 - 0.136: 639 0.136 - 0.204: 25 0.204 - 0.271: 3 0.271 - 0.339: 5 Chirality restraints: 4053 Sorted by residual: chirality pdb=" C1 NAG G1209 " pdb=" ND2 ASN G 709 " pdb=" C2 NAG G1209 " pdb=" O5 NAG G1209 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C1 NAG A1211 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1211 " pdb=" O5 NAG A1211 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 4050 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1207 " 0.282 2.00e-02 2.50e+03 2.37e-01 7.04e+02 pdb=" C7 NAG C1207 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG C1207 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG C1207 " -0.405 2.00e-02 2.50e+03 pdb=" O7 NAG C1207 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " 0.046 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO A 217 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 353 " -0.016 2.00e-02 2.50e+03 1.56e-02 6.12e+00 pdb=" CG TRP G 353 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP G 353 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP G 353 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 353 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 353 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 353 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 353 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 353 " -0.000 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 246 2.64 - 3.20: 21913 3.20 - 3.77: 36268 3.77 - 4.33: 48554 4.33 - 4.90: 80620 Nonbonded interactions: 187601 Sorted by model distance: nonbonded pdb=" CB CYS C 617 " pdb=" CG2 VAL C 620 " model vdw 2.074 3.860 nonbonded pdb=" OH TYR G 369 " pdb=" O PRO G 384 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR G 323 " pdb=" OE1 GLU G 324 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLN A 134 " pdb=" OG SER A 161 " model vdw 2.254 3.040 ... (remaining 187596 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } 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: 8.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.550 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.004 0.097 25392 Z= 0.211 Angle : 0.795 12.789 34644 Z= 0.424 Chirality : 0.050 0.339 4053 Planarity : 0.006 0.237 4392 Dihedral : 13.331 89.633 9867 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.16 (0.15), residues: 3027 helix: 1.60 (0.22), residues: 630 sheet: 0.55 (0.20), residues: 659 loop : -1.05 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 408 TYR 0.040 0.001 TYR G 904 PHE 0.028 0.002 PHE C 201 TRP 0.043 0.001 TRP G 353 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00398 (25302) covalent geometry : angle 0.75705 (34413) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.50611 ( 78) hydrogen bonds : bond 0.23546 ( 854) hydrogen bonds : angle 7.83632 ( 2457) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 1.10385 ( 9) link_NAG-ASN : bond 0.00614 ( 48) link_NAG-ASN : angle 3.72998 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.7743 time to fit residues: 64.4245 Evaluate side-chains 40 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 540 ASN A 613 GLN A 762 GLN A 992 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** G 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN G 460 ASN G 703 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.053403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.030648 restraints weight = 205332.799| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 6.76 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25392 Z= 0.261 Angle : 0.713 17.300 34644 Z= 0.355 Chirality : 0.047 0.363 4053 Planarity : 0.004 0.049 4392 Dihedral : 8.231 59.041 4356 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.38 % 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 (0.15), residues: 3027 helix: 1.94 (0.22), residues: 672 sheet: 0.42 (0.20), residues: 681 loop : -1.00 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 408 TYR 0.029 0.001 TYR G 369 PHE 0.019 0.002 PHE C 400 TRP 0.015 0.001 TRP G 353 HIS 0.009 0.001 HIS G 519 Details of bonding type rmsd covalent geometry : bond 0.00579 (25302) covalent geometry : angle 0.67974 (34413) SS BOND : bond 0.00422 ( 39) SS BOND : angle 1.54175 ( 78) hydrogen bonds : bond 0.05837 ( 854) hydrogen bonds : angle 5.94472 ( 2457) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 1.08929 ( 9) link_NAG-ASN : bond 0.00538 ( 48) link_NAG-ASN : angle 3.25296 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.8949 (tmt) cc_final: 0.8514 (tmt) REVERT: C 869 MET cc_start: 0.9371 (mtt) cc_final: 0.9139 (mtp) REVERT: G 740 MET cc_start: 0.8740 (tmm) cc_final: 0.8519 (tmm) outliers start: 4 outliers final: 0 residues processed: 44 average time/residue: 0.8110 time to fit residues: 41.2085 Evaluate side-chains 35 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 146 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A1071 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 969 ASN G 188 ASN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 926 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.048004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.030834 restraints weight = 225524.503| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 6.04 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25392 Z= 0.232 Angle : 0.655 17.005 34644 Z= 0.326 Chirality : 0.046 0.347 4053 Planarity : 0.004 0.061 4392 Dihedral : 7.574 57.197 4356 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.60 % Allowed : 9.00 % Favored : 90.40 % 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: 0.04 (0.15), residues: 3027 helix: 2.09 (0.21), residues: 666 sheet: 0.29 (0.20), residues: 674 loop : -0.97 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1107 TYR 0.034 0.001 TYR G 904 PHE 0.019 0.001 PHE A 855 TRP 0.014 0.001 TRP A 436 HIS 0.008 0.001 HIS G 519 Details of bonding type rmsd covalent geometry : bond 0.00516 (25302) covalent geometry : angle 0.62496 (34413) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.48287 ( 78) hydrogen bonds : bond 0.05513 ( 854) hydrogen bonds : angle 5.53023 ( 2457) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 1.03571 ( 9) link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.95587 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: C 740 MET cc_start: 0.8902 (tmt) cc_final: 0.8425 (tmt) REVERT: C 869 MET cc_start: 0.9408 (mtt) cc_final: 0.9205 (mtt) REVERT: G 452 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9459 (mm) REVERT: G 740 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8592 (tmm) outliers start: 16 outliers final: 4 residues processed: 53 average time/residue: 0.6053 time to fit residues: 38.4178 Evaluate side-chains 42 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 915 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 211 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.052651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.030747 restraints weight = 206322.577| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 6.53 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25392 Z= 0.128 Angle : 0.587 17.779 34644 Z= 0.287 Chirality : 0.045 0.331 4053 Planarity : 0.004 0.065 4392 Dihedral : 7.219 56.146 4356 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.67 % Allowed : 9.97 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3027 helix: 2.28 (0.22), residues: 664 sheet: 0.36 (0.20), residues: 673 loop : -0.86 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.024 0.001 TYR G 369 PHE 0.015 0.001 PHE C 400 TRP 0.012 0.001 TRP A 436 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00287 (25302) covalent geometry : angle 0.55649 (34413) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.19119 ( 78) hydrogen bonds : bond 0.04607 ( 854) hydrogen bonds : angle 5.21021 ( 2457) link_BETA1-4 : bond 0.00119 ( 3) link_BETA1-4 : angle 0.90688 ( 9) link_NAG-ASN : bond 0.00370 ( 48) link_NAG-ASN : angle 2.86162 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.871 Fit side-chains REVERT: A 233 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8847 (pt) REVERT: C 740 MET cc_start: 0.8958 (tmt) cc_final: 0.8504 (tmt) REVERT: C 869 MET cc_start: 0.9366 (mtt) cc_final: 0.9158 (mtt) REVERT: G 452 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9465 (mm) REVERT: G 740 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8643 (tmm) outliers start: 18 outliers final: 3 residues processed: 52 average time/residue: 0.5731 time to fit residues: 35.8597 Evaluate side-chains 39 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 740 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 203 optimal weight: 6.9990 chunk 294 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 907 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 913 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.048284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.033212 restraints weight = 230744.284| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 6.32 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25392 Z= 0.098 Angle : 0.563 16.741 34644 Z= 0.273 Chirality : 0.044 0.322 4053 Planarity : 0.004 0.068 4392 Dihedral : 6.874 55.663 4356 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.60 % Allowed : 10.71 % Favored : 88.69 % 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: 0.33 (0.16), residues: 3027 helix: 2.45 (0.22), residues: 659 sheet: 0.41 (0.20), residues: 680 loop : -0.79 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.018 0.001 TYR G 369 PHE 0.013 0.001 PHE C 400 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00217 (25302) covalent geometry : angle 0.53542 (34413) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.01403 ( 78) hydrogen bonds : bond 0.04007 ( 854) hydrogen bonds : angle 4.94736 ( 2457) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 0.86616 ( 9) link_NAG-ASN : bond 0.00437 ( 48) link_NAG-ASN : angle 2.67532 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.969 Fit side-chains REVERT: C 740 MET cc_start: 0.8972 (tmt) cc_final: 0.8527 (tmt) REVERT: C 869 MET cc_start: 0.9377 (mtt) cc_final: 0.9157 (mtp) REVERT: G 452 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9492 (mm) REVERT: G 740 MET cc_start: 0.8855 (tmm) cc_final: 0.8566 (tmm) outliers start: 16 outliers final: 6 residues processed: 51 average time/residue: 0.6593 time to fit residues: 39.7536 Evaluate side-chains 43 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 649 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 16 optimal weight: 5.9990 chunk 249 optimal weight: 0.0370 chunk 92 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 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 = 0.3619 r_free = 0.3619 target = 0.047894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.030827 restraints weight = 225505.686| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 6.10 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25392 Z= 0.214 Angle : 0.606 17.107 34644 Z= 0.297 Chirality : 0.045 0.332 4053 Planarity : 0.004 0.068 4392 Dihedral : 6.946 57.611 4356 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.86 % Allowed : 11.24 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 3027 helix: 2.46 (0.22), residues: 661 sheet: 0.31 (0.20), residues: 644 loop : -0.80 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.020 0.001 TYR C 904 PHE 0.012 0.001 PHE C 168 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00484 (25302) covalent geometry : angle 0.57976 (34413) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.23641 ( 78) hydrogen bonds : bond 0.04712 ( 854) hydrogen bonds : angle 5.10804 ( 2457) link_BETA1-4 : bond 0.00040 ( 3) link_BETA1-4 : angle 0.98118 ( 9) link_NAG-ASN : bond 0.00376 ( 48) link_NAG-ASN : angle 2.68095 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 37 time to evaluate : 0.937 Fit side-chains REVERT: C 740 MET cc_start: 0.8965 (tmt) cc_final: 0.8486 (tmt) REVERT: G 452 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9478 (mm) REVERT: G 613 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8959 (mp10) REVERT: G 740 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8625 (tmm) outliers start: 23 outliers final: 7 residues processed: 58 average time/residue: 0.5577 time to fit residues: 39.0688 Evaluate side-chains 45 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 915 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 39 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.067709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052099 restraints weight = 201224.219| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 7.38 r_work: 0.2862 rms_B_bonded: 6.98 restraints_weight: 2.0000 r_work: 0.2940 rms_B_bonded: 5.33 restraints_weight: 4.0000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25392 Z= 0.173 Angle : 0.599 17.436 34644 Z= 0.290 Chirality : 0.045 0.332 4053 Planarity : 0.004 0.069 4392 Dihedral : 6.910 56.545 4356 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.89 % Allowed : 11.90 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 3027 helix: 2.47 (0.22), residues: 662 sheet: 0.29 (0.20), residues: 640 loop : -0.82 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.016 0.001 TYR C 904 PHE 0.010 0.001 PHE G 133 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS G 655 Details of bonding type rmsd covalent geometry : bond 0.00386 (25302) covalent geometry : angle 0.57321 (34413) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.30982 ( 78) hydrogen bonds : bond 0.04589 ( 854) hydrogen bonds : angle 5.06117 ( 2457) link_BETA1-4 : bond 0.00083 ( 3) link_BETA1-4 : angle 0.92904 ( 9) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.63693 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.989 Fit side-chains REVERT: A 533 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9008 (pp) REVERT: C 740 MET cc_start: 0.9279 (tmt) cc_final: 0.8743 (tmt) REVERT: G 452 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9459 (mm) REVERT: G 613 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.9085 (mp10) REVERT: G 740 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8886 (tmm) outliers start: 24 outliers final: 11 residues processed: 59 average time/residue: 0.5550 time to fit residues: 39.5906 Evaluate side-chains 50 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 915 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 166 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.047863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.030952 restraints weight = 225436.405| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 6.33 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25392 Z= 0.157 Angle : 0.602 17.655 34644 Z= 0.289 Chirality : 0.045 0.327 4053 Planarity : 0.004 0.069 4392 Dihedral : 6.952 56.544 4356 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.93 % Allowed : 12.09 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 3027 helix: 2.53 (0.22), residues: 659 sheet: 0.30 (0.20), residues: 642 loop : -0.79 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.023 0.001 TYR C 904 PHE 0.010 0.001 PHE G 133 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS G 655 Details of bonding type rmsd covalent geometry : bond 0.00354 (25302) covalent geometry : angle 0.56601 (34413) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.28480 ( 78) hydrogen bonds : bond 0.04497 ( 854) hydrogen bonds : angle 5.01571 ( 2457) link_BETA1-4 : bond 0.00100 ( 3) link_BETA1-4 : angle 0.91158 ( 9) link_NAG-ASN : bond 0.00352 ( 48) link_NAG-ASN : angle 3.12803 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.945 Fit side-chains REVERT: A 533 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 740 MET cc_start: 0.8950 (tmt) cc_final: 0.8430 (tmt) REVERT: G 452 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9488 (mm) REVERT: G 553 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9121 (t) REVERT: G 613 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8993 (mp10) REVERT: G 740 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8603 (tmm) outliers start: 25 outliers final: 11 residues processed: 60 average time/residue: 0.5138 time to fit residues: 37.4306 Evaluate side-chains 52 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain G residue 915 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 173 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 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 = 0.3768 r_free = 0.3768 target = 0.051997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.030257 restraints weight = 210696.316| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 6.48 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25392 Z= 0.137 Angle : 0.600 17.644 34644 Z= 0.286 Chirality : 0.045 0.440 4053 Planarity : 0.004 0.069 4392 Dihedral : 6.863 56.140 4356 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.67 % Allowed : 12.28 % Favored : 87.05 % 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: 0.34 (0.16), residues: 3027 helix: 2.50 (0.22), residues: 665 sheet: 0.35 (0.20), residues: 643 loop : -0.77 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.018 0.001 TYR C 904 PHE 0.011 0.001 PHE G 133 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS G 655 Details of bonding type rmsd covalent geometry : bond 0.00311 (25302) covalent geometry : angle 0.56346 (34413) SS BOND : bond 0.00262 ( 39) SS BOND : angle 1.34878 ( 78) hydrogen bonds : bond 0.04320 ( 854) hydrogen bonds : angle 4.94483 ( 2457) link_BETA1-4 : bond 0.00148 ( 3) link_BETA1-4 : angle 0.88908 ( 9) link_NAG-ASN : bond 0.00522 ( 48) link_NAG-ASN : angle 3.09554 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.903 Fit side-chains REVERT: A 166 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8275 (m) REVERT: A 533 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9089 (pp) REVERT: C 740 MET cc_start: 0.8952 (tmt) cc_final: 0.8425 (tmt) REVERT: G 553 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9138 (t) REVERT: G 613 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9020 (mp10) REVERT: G 740 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8626 (tmm) outliers start: 18 outliers final: 8 residues processed: 53 average time/residue: 0.5829 time to fit residues: 36.8760 Evaluate side-chains 49 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 2 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 239 optimal weight: 0.0570 chunk 48 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 chunk 223 optimal weight: 9.9990 chunk 302 optimal weight: 0.0470 chunk 137 optimal weight: 7.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 GLN ** 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 = 0.3778 r_free = 0.3778 target = 0.052262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.031047 restraints weight = 210380.439| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 6.99 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25392 Z= 0.106 Angle : 0.591 17.270 34644 Z= 0.279 Chirality : 0.045 0.410 4053 Planarity : 0.004 0.071 4392 Dihedral : 6.762 56.103 4356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.48 % Allowed : 12.61 % Favored : 86.90 % 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: 0.39 (0.16), residues: 3027 helix: 2.54 (0.22), residues: 664 sheet: 0.42 (0.20), residues: 646 loop : -0.75 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.015 0.001 TYR G 369 PHE 0.011 0.001 PHE C 400 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS G 655 Details of bonding type rmsd covalent geometry : bond 0.00238 (25302) covalent geometry : angle 0.55481 (34413) SS BOND : bond 0.00248 ( 39) SS BOND : angle 1.19676 ( 78) hydrogen bonds : bond 0.04000 ( 854) hydrogen bonds : angle 4.82149 ( 2457) link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 0.87431 ( 9) link_NAG-ASN : bond 0.00492 ( 48) link_NAG-ASN : angle 3.09074 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.881 Fit side-chains REVERT: A 533 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9094 (pp) REVERT: C 740 MET cc_start: 0.8970 (tmt) cc_final: 0.8427 (tmt) REVERT: G 553 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9141 (t) REVERT: G 613 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.9065 (mp10) REVERT: G 740 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8637 (tmm) outliers start: 13 outliers final: 8 residues processed: 48 average time/residue: 0.6538 time to fit residues: 37.5030 Evaluate side-chains 47 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 299 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN G 164 ASN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.047435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.032422 restraints weight = 235907.991| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 6.41 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25392 Z= 0.232 Angle : 0.648 17.603 34644 Z= 0.312 Chirality : 0.045 0.420 4053 Planarity : 0.004 0.068 4392 Dihedral : 6.897 57.844 4356 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.67 % Allowed : 12.50 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 3027 helix: 2.34 (0.22), residues: 672 sheet: 0.17 (0.20), residues: 655 loop : -0.79 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.022 0.001 TYR C 904 PHE 0.015 0.001 PHE G 168 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS G 655 Details of bonding type rmsd covalent geometry : bond 0.00519 (25302) covalent geometry : angle 0.61389 (34413) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.44864 ( 78) hydrogen bonds : bond 0.04839 ( 854) hydrogen bonds : angle 5.07450 ( 2457) link_BETA1-4 : bond 0.00081 ( 3) link_BETA1-4 : angle 1.00472 ( 9) link_NAG-ASN : bond 0.00497 ( 48) link_NAG-ASN : angle 3.10319 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8052.08 seconds wall clock time: 137 minutes 51.46 seconds (8271.46 seconds total)