Starting phenix.real_space_refine on Tue Aug 26 01:59:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gdr_29950/08_2025/8gdr_29950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gdr_29950/08_2025/8gdr_29950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gdr_29950/08_2025/8gdr_29950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gdr_29950/08_2025/8gdr_29950.map" model { file = "/net/cci-nas-00/data/ceres_data/8gdr_29950/08_2025/8gdr_29950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gdr_29950/08_2025/8gdr_29950.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.095 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 144 5.16 5 C 20542 2.51 5 N 5339 2.21 5 O 6306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32331 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Chain: "C" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1694 Classifications: {'peptide': 224} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 208} Chain: "D" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1604 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain: "E" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "F" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "H" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1694 Classifications: {'peptide': 224} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 208} Chain: "J" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1604 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain: "c" 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: "g" 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: "i" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.80, per 1000 atoms: 0.24 Number of scatterers: 32331 At special positions: 0 Unit cell: (155.555, 167.196, 243.386, 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 144 16.00 O 6306 8.00 N 5339 7.00 C 20542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.04 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 197 " 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 c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 616 " " NAG A1204 " - " ASN A 709 " " NAG A1205 " - " ASN A 717 " " NAG A1206 " - " ASN A1098 " " NAG A1207 " - " ASN A1134 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 801 " " NAG A1210 " - " ASN A1074 " " NAG E1201 " - " ASN E 282 " " NAG E1202 " - " ASN E 657 " " NAG E1203 " - " ASN E 616 " " NAG E1204 " - " ASN E 709 " " NAG E1205 " - " ASN E1074 " " NAG E1206 " - " ASN E 603 " " NAG E1207 " - " ASN E 343 " " NAG F1201 " - " ASN F 331 " " NAG F1202 " - " ASN F 603 " " NAG F1203 " - " ASN F 616 " " NAG F1204 " - " ASN F 657 " " NAG F1205 " - " ASN F 709 " " NAG F1206 " - " ASN F 717 " " NAG F1207 " - " ASN F1134 " " NAG F1208 " - " ASN F 343 " " NAG F1209 " - " ASN F1098 " " NAG F1210 " - " ASN F1074 " " NAG F1211 " - " ASN F 801 " " NAG c 1 " - " ASN E1134 " " NAG e 1 " - " ASN E1098 " " NAG g 1 " - " ASN E 717 " " NAG i 1 " - " ASN E 801 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7666 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 75 sheets defined 21.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 294 through 303 Processing helix 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: 3.656A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.085A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.429A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.623A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.219A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.988A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.963A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.877A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'D' and resid 125 through 131 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.962A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 4.242A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 619 through 623 Processing helix chain 'E' and resid 631 through 639 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 removed outlier: 4.265A pdb=" N LEU E 752 " --> pdb=" O GLU E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.646A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.581A pdb=" N GLY E 885 " --> pdb=" O THR E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 891 removed outlier: 4.277A pdb=" N GLY E 891 " --> pdb=" O PHE E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 918 removed outlier: 4.292A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.687A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.972A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1032 removed outlier: 4.926A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1149 Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 337 through 343 removed outlier: 3.773A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 365 through 370 removed outlier: 3.737A pdb=" N TYR F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.586A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP F 389 " --> pdb=" O LYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.571A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU F 752 " --> pdb=" O GLU F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.531A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 801 through 805 removed outlier: 4.312A pdb=" N GLN F 804 " --> pdb=" O ASN F 801 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 825 Processing helix chain 'F' and resid 851 through 856 removed outlier: 3.618A pdb=" N LYS F 854 " --> pdb=" O CYS F 851 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE F 855 " --> pdb=" O ALA F 852 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN F 856 " --> pdb=" O GLN F 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 851 through 856' Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 913 through 918 removed outlier: 3.607A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 939 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.722A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 984 removed outlier: 3.536A pdb=" N ILE F 980 " --> pdb=" O VAL F 976 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.521A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1146 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.625A pdb=" N LYS J 85 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 131 Processing helix chain 'J' and resid 185 through 192 Processing helix chain 'J' and resid 211 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.124A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.703A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.858A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 5.336A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.492A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.038A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.695A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.812A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.828A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.668A pdb=" N VAL C 12 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.668A pdb=" N VAL C 12 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR C 108 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR C 101 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE C 106 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.175A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.175A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AC6, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AC7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC8, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.360A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.120A pdb=" N TYR D 176 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.120A pdb=" N TYR D 176 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.455A pdb=" N TRP D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.210A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA E 263 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR E 95 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 28 through 31 Processing sheet with id=AD5, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.544A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.416A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 156 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N TYR E 144 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU E 154 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS E 146 " --> pdb=" O TRP E 152 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP E 152 " --> pdb=" O HIS E 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.932A pdb=" N ARG E 237 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE E 106 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN E 239 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP E 104 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU E 241 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.653A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 324 through 328 removed outlier: 4.093A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.527A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.610A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.507A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 575 through 577 Processing sheet with id=AE6, first strand: chain 'E' and resid 653 through 655 removed outlier: 3.611A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 711 through 727 removed outlier: 6.934A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E1052 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.458A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.251A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA F 27 " --> pdb=" O TRP F 64 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA F 27 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.724A pdb=" N ASP F 53 " --> pdb=" O ARG F 273 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 273 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.978A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY F 142 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS F 146 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER F 151 " --> pdb=" O HIS F 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.945A pdb=" N ARG F 237 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE F 106 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN F 239 " --> pdb=" O TRP F 104 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP F 104 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 241 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 126 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL F 171 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE F 128 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU F 169 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL F 130 " --> pdb=" O THR F 167 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 134 through 135 removed outlier: 7.139A pdb=" N GLN F 134 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 314 through 319 removed outlier: 6.378A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AG1, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AG2, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.255A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AG4, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 711 through 718 removed outlier: 6.481A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F1076 " --> pdb=" O SER F1097 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS F1101 " --> pdb=" O ASN F1098 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 721 through 723 Processing sheet with id=AG7, first strand: chain 'F' and resid 721 through 723 removed outlier: 6.748A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 1120 through 1122 Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.181A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP H 74 " --> pdb=" O GLN H 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.818A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.236A pdb=" N TYR H 108 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR H 101 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE H 106 " --> pdb=" O THR H 101 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 126 through 129 removed outlier: 5.772A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 126 through 129 removed outlier: 5.772A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.592A pdb=" N VAL J 10 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.592A pdb=" N VAL J 10 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AI1, first strand: chain 'J' and resid 118 through 122 removed outlier: 6.504A pdb=" N TYR J 176 " --> pdb=" O ASP J 142 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 118 through 122 removed outlier: 6.504A pdb=" N TYR J 176 " --> pdb=" O ASP J 142 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 157 through 158 1335 hydrogen bonds defined for protein. 3492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.89 Time building geometry restraints manager: 3.69 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: 10310 1.34 - 1.46: 8108 1.46 - 1.58: 14484 1.58 - 1.71: 3 1.71 - 1.83: 182 Bond restraints: 33087 Sorted by residual: bond pdb=" N GLN A 675 " pdb=" CA GLN A 675 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.56e+00 bond pdb=" CB PRO J 7 " pdb=" CG PRO J 7 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.77e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.53e+00 bond pdb=" CB PRO J 57 " pdb=" CG PRO J 57 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.34e+00 ... (remaining 33082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 44543 2.26 - 4.52: 496 4.52 - 6.77: 28 6.77 - 9.03: 2 9.03 - 11.29: 1 Bond angle restraints: 45070 Sorted by residual: angle pdb=" CA PRO J 57 " pdb=" N PRO J 57 " pdb=" CD PRO J 57 " ideal model delta sigma weight residual 112.00 100.71 11.29 1.40e+00 5.10e-01 6.50e+01 angle pdb=" CA PRO J 7 " pdb=" N PRO J 7 " pdb=" CD PRO J 7 " ideal model delta sigma weight residual 112.00 103.39 8.61 1.40e+00 5.10e-01 3.78e+01 angle pdb=" CA PRO F 521 " pdb=" N PRO F 521 " pdb=" CD PRO F 521 " ideal model delta sigma weight residual 112.00 104.34 7.66 1.40e+00 5.10e-01 2.99e+01 angle pdb=" CA PRO J 46 " pdb=" N PRO J 46 " pdb=" CD PRO J 46 " ideal model delta sigma weight residual 112.00 105.68 6.32 1.40e+00 5.10e-01 2.04e+01 angle pdb=" N PRO J 57 " pdb=" CD PRO J 57 " pdb=" CG PRO J 57 " ideal model delta sigma weight residual 103.20 97.74 5.46 1.50e+00 4.44e-01 1.33e+01 ... (remaining 45065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17779 17.93 - 35.86: 1840 35.86 - 53.78: 417 53.78 - 71.71: 78 71.71 - 89.64: 41 Dihedral angle restraints: 20155 sinusoidal: 8224 harmonic: 11931 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 7.33 85.67 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS F 662 " pdb=" SG CYS F 662 " pdb=" SG CYS F 671 " pdb=" CB CYS F 671 " ideal model delta sinusoidal sigma weight residual -86.00 -18.92 -67.08 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -35.83 -50.17 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 20152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.769: 5230 0.769 - 1.537: 0 1.537 - 2.306: 0 2.306 - 3.075: 0 3.075 - 3.844: 2 Chirality restraints: 5232 Sorted by residual: chirality pdb=" C1 NAG E1207 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E1207 " pdb=" O5 NAG E1207 " both_signs ideal model delta sigma weight residual False -2.40 1.44 -3.84 2.00e-01 2.50e+01 3.69e+02 chirality pdb=" C1 NAG A1209 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1209 " pdb=" O5 NAG A1209 " both_signs ideal model delta sigma weight residual False -2.40 1.39 -3.79 2.00e-01 2.50e+01 3.60e+02 chirality pdb=" C1 NAG A1206 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1206 " pdb=" O5 NAG A1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 5229 not shown) Planarity restraints: 5799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " -0.126 2.00e-02 2.50e+03 1.17e-01 1.71e+02 pdb=" CG ASN E 343 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " 0.177 2.00e-02 2.50e+03 pdb=" C1 NAG E1207 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " -0.122 2.00e-02 2.50e+03 1.13e-01 1.60e+02 pdb=" CG ASN A 801 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " 0.148 2.00e-02 2.50e+03 pdb=" C1 NAG A1209 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG J 56 " 0.102 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO J 57 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO J 57 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO J 57 " 0.075 5.00e-02 4.00e+02 ... (remaining 5796 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 220 2.46 - 3.07: 23669 3.07 - 3.68: 47240 3.68 - 4.29: 68910 4.29 - 4.90: 117227 Nonbonded interactions: 257266 Sorted by model distance: nonbonded pdb=" O ILE C 105 " pdb=" OH TYR D 38 " model vdw 1.856 3.040 nonbonded pdb=" OD1 ASN F 354 " pdb=" OG SER F 399 " model vdw 1.900 3.040 nonbonded pdb=" OG SER E 359 " pdb=" OG1 THR E 523 " model vdw 1.930 3.040 nonbonded pdb=" OD1 ASP C 74 " pdb=" OG SER C 76 " model vdw 1.948 3.040 nonbonded pdb=" OD2 ASP F 398 " pdb=" OH TYR F 423 " model vdw 1.951 3.040 ... (remaining 257261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1204 through 1210)) selection = (chain 'E' and (resid 14 through 617 or resid 641 through 827 or resid 852 throu \ gh 940 or resid 944 through 1146 or resid 1201 through 1207)) selection = (chain 'F' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1204 through 1210)) } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.640 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.870 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.396 33146 Z= 0.216 Angle : 0.600 23.304 45224 Z= 0.306 Chirality : 0.087 3.844 5232 Planarity : 0.005 0.146 5767 Dihedral : 15.480 89.638 12420 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.47 % Allowed : 19.64 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -1.02 (0.13), residues: 4062 helix: 0.53 (0.21), residues: 676 sheet: -0.47 (0.16), residues: 1065 loop : -1.14 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 68 TYR 0.017 0.001 TYR D 51 PHE 0.025 0.001 PHE E 562 TRP 0.007 0.001 TRP H 49 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00369 (33087) covalent geometry : angle 0.56749 (45070) SS BOND : bond 0.00446 ( 23) SS BOND : angle 1.07221 ( 46) hydrogen bonds : bond 0.12274 ( 1249) hydrogen bonds : angle 7.60007 ( 3492) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 3.06390 ( 12) link_NAG-ASN : bond 0.09082 ( 32) link_NAG-ASN : angle 4.11673 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 527 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 909 ILE cc_start: 0.9050 (pt) cc_final: 0.8766 (pt) REVERT: A 1050 MET cc_start: 0.9022 (ptm) cc_final: 0.8793 (ptp) REVERT: C 205 ASN cc_start: 0.8625 (t0) cc_final: 0.8359 (t0) REVERT: D 18 ILE cc_start: 0.8847 (mm) cc_final: 0.8645 (mm) REVERT: E 324 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6940 (tm-30) REVERT: E 531 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8328 (p) REVERT: E 869 MET cc_start: 0.8791 (mtp) cc_final: 0.8495 (mtp) REVERT: E 902 MET cc_start: 0.8831 (mmm) cc_final: 0.7882 (tpt) REVERT: E 1126 CYS cc_start: 0.8623 (m) cc_final: 0.8067 (p) REVERT: F 269 TYR cc_start: 0.8154 (m-80) cc_final: 0.7567 (m-80) REVERT: F 978 ASN cc_start: 0.8624 (t0) cc_final: 0.8298 (t0) REVERT: H 59 LYS cc_start: 0.8129 (mttt) cc_final: 0.7872 (mttt) REVERT: H 81 VAL cc_start: 0.6682 (t) cc_final: 0.6476 (m) REVERT: H 111 GLN cc_start: 0.6103 (tp-100) cc_final: 0.5183 (pt0) REVERT: J 44 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6572 (mmmt) outliers start: 17 outliers final: 10 residues processed: 536 average time/residue: 0.1685 time to fit residues: 150.8351 Evaluate side-chains 514 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 503 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 1098 ASN Chi-restraints excluded: chain H residue 170 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 314 GLN A 580 GLN A 690 GLN A 762 GLN A1005 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN D 41 HIS D 130 GLN D 188 GLN E 30 ASN E 61 ASN E 115 GLN E 207 HIS E 360 ASN E 907 ASN E 955 ASN E 969 ASN E1088 HIS F 66 HIS F 360 ASN F 450 ASN F 498 GLN F 907 ASN F1010 GLN H 1 GLN H 99 GLN H 161 ASN J 41 HIS J 192 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.216604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.128988 restraints weight = 39929.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.131336 restraints weight = 23327.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.131630 restraints weight = 14433.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.132423 restraints weight = 15034.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.132624 restraints weight = 13122.772| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33146 Z= 0.214 Angle : 0.658 21.558 45224 Z= 0.330 Chirality : 0.049 0.663 5232 Planarity : 0.005 0.070 5767 Dihedral : 6.684 58.883 5164 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.02 % Allowed : 17.77 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.64 (0.13), residues: 4062 helix: 1.23 (0.20), residues: 673 sheet: -0.32 (0.15), residues: 1078 loop : -0.97 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 68 TYR 0.028 0.001 TYR D 51 PHE 0.024 0.002 PHE F 497 TRP 0.011 0.001 TRP D 189 HIS 0.006 0.001 HIS E 655 Details of bonding type rmsd covalent geometry : bond 0.00509 (33087) covalent geometry : angle 0.62837 (45070) SS BOND : bond 0.00363 ( 23) SS BOND : angle 1.52449 ( 46) hydrogen bonds : bond 0.04393 ( 1249) hydrogen bonds : angle 6.10185 ( 3492) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 2.49849 ( 12) link_NAG-ASN : bond 0.00598 ( 32) link_NAG-ASN : angle 4.07087 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 539 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: A 380 TYR cc_start: 0.8548 (m-80) cc_final: 0.8277 (m-80) REVERT: A 740 MET cc_start: 0.8051 (tpp) cc_final: 0.7780 (mmt) REVERT: A 931 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 935 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: A 979 ASP cc_start: 0.7331 (t0) cc_final: 0.7129 (t0) REVERT: A 1074 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8260 (p0) REVERT: C 147 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7376 (tp) REVERT: C 205 ASN cc_start: 0.8998 (t0) cc_final: 0.8484 (t0) REVERT: C 215 LYS cc_start: 0.8394 (tppt) cc_final: 0.7827 (ttmt) REVERT: D 49 MET cc_start: 0.7485 (mmt) cc_final: 0.7186 (mmt) REVERT: E 58 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: E 360 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8574 (p0) REVERT: E 531 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8282 (p) REVERT: E 619 GLU cc_start: 0.7987 (mp0) cc_final: 0.7735 (mp0) REVERT: E 737 ASP cc_start: 0.7887 (p0) cc_final: 0.7438 (p0) REVERT: E 748 GLU cc_start: 0.7661 (pm20) cc_final: 0.7388 (pm20) REVERT: E 752 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8721 (tt) REVERT: F 269 TYR cc_start: 0.8179 (m-80) cc_final: 0.7371 (m-80) REVERT: F 364 ASP cc_start: 0.8866 (t0) cc_final: 0.8610 (t0) REVERT: F 558 LYS cc_start: 0.8939 (pttp) cc_final: 0.8612 (pttm) REVERT: F 718 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8796 (p90) REVERT: F 767 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8611 (mt) REVERT: F 978 ASN cc_start: 0.8689 (t0) cc_final: 0.8303 (t0) REVERT: F 985 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7489 (t70) REVERT: H 40 ARG cc_start: 0.7357 (ptt180) cc_final: 0.7044 (ptt90) REVERT: H 59 LYS cc_start: 0.8134 (mttt) cc_final: 0.7784 (mttt) REVERT: H 111 GLN cc_start: 0.5996 (tp-100) cc_final: 0.5104 (pt0) REVERT: J 44 LYS cc_start: 0.7000 (mmmt) cc_final: 0.6632 (mmmt) REVERT: J 49 MET cc_start: 0.7354 (mmt) cc_final: 0.7006 (mmt) outliers start: 144 outliers final: 79 residues processed: 643 average time/residue: 0.1630 time to fit residues: 178.3911 Evaluate side-chains 581 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 490 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 743 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 883 THR Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1105 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 453 TYR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 718 PHE Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 993 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 142 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 113 optimal weight: 0.9980 chunk 123 optimal weight: 0.0040 chunk 276 optimal weight: 8.9990 chunk 333 optimal weight: 0.0770 chunk 235 optimal weight: 0.8980 chunk 273 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 260 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN C 100 HIS C 177 GLN D 130 GLN D 188 GLN E 30 ASN E 188 ASN E 207 HIS E 606 ASN E 907 ASN E 914 ASN ** E1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS J 41 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.217802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.126837 restraints weight = 39756.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131950 restraints weight = 21526.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.135139 restraints weight = 13797.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.135301 restraints weight = 10791.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.135568 restraints weight = 10798.764| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33146 Z= 0.135 Angle : 0.597 13.031 45224 Z= 0.300 Chirality : 0.046 0.468 5232 Planarity : 0.004 0.058 5767 Dihedral : 6.236 56.116 5157 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.93 % Allowed : 18.36 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.42 (0.13), residues: 4062 helix: 1.60 (0.20), residues: 669 sheet: -0.21 (0.16), residues: 1062 loop : -0.87 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 34 TYR 0.023 0.001 TYR D 51 PHE 0.023 0.001 PHE A 168 TRP 0.015 0.001 TRP D 189 HIS 0.004 0.001 HIS E 655 Details of bonding type rmsd covalent geometry : bond 0.00314 (33087) covalent geometry : angle 0.57616 (45070) SS BOND : bond 0.00298 ( 23) SS BOND : angle 1.23249 ( 46) hydrogen bonds : bond 0.03862 ( 1249) hydrogen bonds : angle 5.79245 ( 3492) link_BETA1-4 : bond 0.00463 ( 4) link_BETA1-4 : angle 2.24855 ( 12) link_NAG-ASN : bond 0.00588 ( 32) link_NAG-ASN : angle 3.28947 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 533 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: A 280 ASN cc_start: 0.7896 (t0) cc_final: 0.7675 (t0) REVERT: A 289 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8325 (p) REVERT: A 347 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6603 (t80) REVERT: A 378 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7239 (ttmm) REVERT: A 794 ILE cc_start: 0.7978 (mt) cc_final: 0.7496 (tt) REVERT: A 796 ASP cc_start: 0.7978 (t0) cc_final: 0.7514 (m-30) REVERT: A 821 LEU cc_start: 0.8794 (tp) cc_final: 0.8452 (tt) REVERT: A 909 ILE cc_start: 0.9365 (pt) cc_final: 0.9058 (pt) REVERT: A 918 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 931 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 935 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: A 979 ASP cc_start: 0.7368 (t0) cc_final: 0.7096 (t0) REVERT: C 89 PRO cc_start: 0.8908 (Cg_exo) cc_final: 0.8675 (Cg_endo) REVERT: C 205 ASN cc_start: 0.8967 (t0) cc_final: 0.8412 (t0) REVERT: C 215 LYS cc_start: 0.8407 (tppt) cc_final: 0.7640 (mtmt) REVERT: D 49 MET cc_start: 0.7359 (mmt) cc_final: 0.7020 (mmt) REVERT: D 144 TYR cc_start: 0.8115 (t80) cc_final: 0.7869 (t80) REVERT: E 34 ARG cc_start: 0.8761 (tpp-160) cc_final: 0.8311 (tpp80) REVERT: E 58 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: E 389 ASP cc_start: 0.8844 (p0) cc_final: 0.8533 (m-30) REVERT: E 509 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6727 (mtt90) REVERT: E 528 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7677 (ptpt) REVERT: E 531 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8429 (p) REVERT: E 737 ASP cc_start: 0.7803 (p0) cc_final: 0.7526 (p0) REVERT: E 740 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7734 (ttt) REVERT: E 787 GLN cc_start: 0.8262 (pt0) cc_final: 0.8018 (pt0) REVERT: F 206 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8091 (ttpt) REVERT: F 294 ASP cc_start: 0.8247 (p0) cc_final: 0.7855 (p0) REVERT: F 364 ASP cc_start: 0.8822 (t0) cc_final: 0.8582 (t0) REVERT: F 558 LYS cc_start: 0.9016 (pttp) cc_final: 0.8676 (pttm) REVERT: F 588 THR cc_start: 0.8692 (m) cc_final: 0.8235 (p) REVERT: F 767 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8563 (mt) REVERT: F 823 PHE cc_start: 0.7696 (t80) cc_final: 0.7184 (m-80) REVERT: F 978 ASN cc_start: 0.8620 (t0) cc_final: 0.8253 (t0) REVERT: F 1084 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: H 4 LEU cc_start: 0.6710 (tp) cc_final: 0.6461 (tp) REVERT: H 5 LYS cc_start: 0.4943 (tmtt) cc_final: 0.4695 (tmtt) REVERT: H 40 ARG cc_start: 0.7315 (ptt180) cc_final: 0.7044 (ptt90) REVERT: H 68 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.8028 (mtp-110) REVERT: H 111 GLN cc_start: 0.6005 (tp-100) cc_final: 0.5176 (pt0) REVERT: H 135 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7320 (mmtm) REVERT: J 44 LYS cc_start: 0.7059 (mmmt) cc_final: 0.6745 (mmmt) REVERT: J 49 MET cc_start: 0.7220 (mmt) cc_final: 0.6863 (mmt) REVERT: J 72 MET cc_start: 0.5001 (mmp) cc_final: 0.4643 (mmp) outliers start: 141 outliers final: 92 residues processed: 625 average time/residue: 0.1641 time to fit residues: 174.7958 Evaluate side-chains 602 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 499 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1105 THR Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 907 ASN Chi-restraints excluded: chain F residue 993 ILE Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 279 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 333 optimal weight: 0.0670 chunk 389 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 364 optimal weight: 0.7980 chunk 237 optimal weight: 0.0670 chunk 143 optimal weight: 9.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 955 ASN C 177 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 188 GLN E 188 ASN E 907 ASN E 920 GLN E 935 GLN E1119 ASN H 1 GLN J 41 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.216693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.127169 restraints weight = 39758.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.130461 restraints weight = 24042.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131841 restraints weight = 15048.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.132468 restraints weight = 13044.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.133296 restraints weight = 13001.479| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33146 Z= 0.206 Angle : 0.613 12.457 45224 Z= 0.309 Chirality : 0.047 0.440 5232 Planarity : 0.004 0.059 5767 Dihedral : 6.140 56.683 5156 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.83 % Allowed : 18.55 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.49 (0.13), residues: 4062 helix: 1.50 (0.20), residues: 668 sheet: -0.24 (0.15), residues: 1088 loop : -0.92 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 319 TYR 0.030 0.001 TYR D 51 PHE 0.025 0.001 PHE A 541 TRP 0.014 0.001 TRP C 109 HIS 0.004 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00491 (33087) covalent geometry : angle 0.59306 (45070) SS BOND : bond 0.00318 ( 23) SS BOND : angle 1.47533 ( 46) hydrogen bonds : bond 0.03981 ( 1249) hydrogen bonds : angle 5.73301 ( 3492) link_BETA1-4 : bond 0.00321 ( 4) link_BETA1-4 : angle 2.17254 ( 12) link_NAG-ASN : bond 0.00732 ( 32) link_NAG-ASN : angle 3.23775 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 517 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: A 280 ASN cc_start: 0.7959 (t0) cc_final: 0.7734 (t0) REVERT: A 289 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 347 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 740 MET cc_start: 0.7917 (tpp) cc_final: 0.7593 (mmt) REVERT: A 794 ILE cc_start: 0.8021 (mt) cc_final: 0.7523 (tt) REVERT: A 796 ASP cc_start: 0.7968 (t0) cc_final: 0.7509 (m-30) REVERT: A 909 ILE cc_start: 0.9055 (pt) cc_final: 0.8815 (pt) REVERT: A 918 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: A 931 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8676 (tt) REVERT: A 935 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: A 979 ASP cc_start: 0.7458 (t0) cc_final: 0.7167 (t0) REVERT: C 205 ASN cc_start: 0.9024 (t0) cc_final: 0.8449 (t0) REVERT: C 215 LYS cc_start: 0.8416 (tppt) cc_final: 0.7654 (mtmt) REVERT: E 34 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8463 (tpp80) REVERT: E 58 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: E 318 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7998 (p90) REVERT: E 389 ASP cc_start: 0.8874 (p0) cc_final: 0.8594 (m-30) REVERT: E 531 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8406 (p) REVERT: E 737 ASP cc_start: 0.7792 (p0) cc_final: 0.7475 (p0) REVERT: E 740 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7798 (ttt) REVERT: E 883 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.8976 (p) REVERT: E 988 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7770 (tm-30) REVERT: F 53 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: F 94 SER cc_start: 0.8245 (t) cc_final: 0.7941 (m) REVERT: F 206 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8195 (ttmt) REVERT: F 239 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: F 274 THR cc_start: 0.7333 (m) cc_final: 0.6943 (p) REVERT: F 357 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7632 (ttp80) REVERT: F 390 LEU cc_start: 0.8916 (mm) cc_final: 0.8655 (mm) REVERT: F 558 LYS cc_start: 0.8970 (pttp) cc_final: 0.8617 (pttm) REVERT: F 651 ILE cc_start: 0.9280 (tp) cc_final: 0.8937 (mt) REVERT: F 718 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8847 (p90) REVERT: F 767 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (mt) REVERT: F 823 PHE cc_start: 0.7768 (t80) cc_final: 0.7351 (m-80) REVERT: F 978 ASN cc_start: 0.8583 (t0) cc_final: 0.8221 (t0) REVERT: F 1084 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: H 40 ARG cc_start: 0.7360 (ptt180) cc_final: 0.7058 (ptt90) REVERT: H 59 LYS cc_start: 0.8188 (mttt) cc_final: 0.7878 (mttt) REVERT: J 49 MET cc_start: 0.7306 (mmt) cc_final: 0.6974 (mmt) REVERT: J 72 MET cc_start: 0.5039 (mmp) cc_final: 0.4174 (mmp) outliers start: 173 outliers final: 117 residues processed: 631 average time/residue: 0.1517 time to fit residues: 163.8337 Evaluate side-chains 628 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 495 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 743 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 794 ILE Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 883 THR Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain E residue 982 SER Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1105 THR Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 718 PHE Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 907 ASN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1081 ILE Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1116 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 9 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 347 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 380 optimal weight: 0.0040 chunk 247 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 311 optimal weight: 0.0570 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 804 GLN A 935 GLN A 955 ASN D 130 GLN D 171 GLN E 907 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 613 GLN F 762 GLN F 992 GLN F1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.219021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.127869 restraints weight = 39570.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.133253 restraints weight = 20968.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.134994 restraints weight = 14311.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.137733 restraints weight = 11803.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.137631 restraints weight = 9293.549| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33146 Z= 0.123 Angle : 0.581 12.685 45224 Z= 0.290 Chirality : 0.045 0.362 5232 Planarity : 0.004 0.059 5767 Dihedral : 5.866 54.534 5156 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.46 % Allowed : 19.39 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.37 (0.13), residues: 4062 helix: 1.63 (0.20), residues: 673 sheet: -0.13 (0.16), residues: 1072 loop : -0.86 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.022 0.001 TYR D 51 PHE 0.024 0.001 PHE A 541 TRP 0.018 0.001 TRP D 189 HIS 0.003 0.001 HIS J 40 Details of bonding type rmsd covalent geometry : bond 0.00286 (33087) covalent geometry : angle 0.56237 (45070) SS BOND : bond 0.00272 ( 23) SS BOND : angle 1.24482 ( 46) hydrogen bonds : bond 0.03588 ( 1249) hydrogen bonds : angle 5.52462 ( 3492) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 2.13074 ( 12) link_NAG-ASN : bond 0.00632 ( 32) link_NAG-ASN : angle 3.02798 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 530 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8091 (t0) cc_final: 0.7775 (t0) REVERT: A 347 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6575 (t80) REVERT: A 378 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7394 (ttmm) REVERT: A 794 ILE cc_start: 0.7997 (mt) cc_final: 0.7517 (tt) REVERT: A 796 ASP cc_start: 0.7947 (t0) cc_final: 0.7534 (m-30) REVERT: A 823 PHE cc_start: 0.7796 (t80) cc_final: 0.7589 (t80) REVERT: A 864 LEU cc_start: 0.8670 (tt) cc_final: 0.8326 (tt) REVERT: A 918 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: A 935 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: A 979 ASP cc_start: 0.7449 (t0) cc_final: 0.7128 (t0) REVERT: C 177 GLN cc_start: 0.7860 (mp-120) cc_final: 0.7625 (mp10) REVERT: C 206 HIS cc_start: 0.6554 (t-90) cc_final: 0.6204 (t-90) REVERT: C 215 LYS cc_start: 0.8373 (tppt) cc_final: 0.7738 (mtmt) REVERT: D 49 MET cc_start: 0.7386 (mmt) cc_final: 0.7073 (mmt) REVERT: E 58 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: E 318 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7722 (p90) REVERT: E 389 ASP cc_start: 0.8823 (p0) cc_final: 0.8618 (m-30) REVERT: E 528 LYS cc_start: 0.7987 (ptpt) cc_final: 0.7101 (ttmt) REVERT: E 531 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8501 (p) REVERT: E 737 ASP cc_start: 0.7796 (p0) cc_final: 0.7442 (p0) REVERT: E 740 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7724 (ttt) REVERT: E 787 GLN cc_start: 0.8270 (pt0) cc_final: 0.7984 (pt0) REVERT: E 988 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7663 (tm-30) REVERT: F 53 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: F 206 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8221 (ttmt) REVERT: F 239 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: F 298 GLU cc_start: 0.7716 (tt0) cc_final: 0.7489 (tt0) REVERT: F 319 ARG cc_start: 0.7435 (ptp-110) cc_final: 0.7205 (ptp-110) REVERT: F 357 ARG cc_start: 0.7887 (ptm-80) cc_final: 0.7513 (ttp80) REVERT: F 558 LYS cc_start: 0.8955 (pttp) cc_final: 0.8628 (pttm) REVERT: F 823 PHE cc_start: 0.7698 (t80) cc_final: 0.7309 (m-80) REVERT: F 909 ILE cc_start: 0.9171 (pt) cc_final: 0.8867 (pt) REVERT: F 957 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: F 978 ASN cc_start: 0.8490 (t0) cc_final: 0.8176 (t0) REVERT: F 1084 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: H 5 LYS cc_start: 0.5198 (tmtt) cc_final: 0.4984 (tmtt) REVERT: H 40 ARG cc_start: 0.7329 (ptt180) cc_final: 0.7053 (ptt90) REVERT: H 59 LYS cc_start: 0.8094 (mttt) cc_final: 0.7816 (mttt) REVERT: H 111 GLN cc_start: 0.6356 (tp-100) cc_final: 0.5555 (mt0) REVERT: H 135 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7125 (mmtm) REVERT: J 49 MET cc_start: 0.7312 (mmt) cc_final: 0.6951 (mmt) REVERT: J 72 MET cc_start: 0.4987 (mmp) cc_final: 0.4509 (mmp) outliers start: 160 outliers final: 108 residues processed: 642 average time/residue: 0.1526 time to fit residues: 167.2240 Evaluate side-chains 618 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 499 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 1082 CYS Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 957 GLN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 331 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 214 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 chunk 271 optimal weight: 40.0000 chunk 340 optimal weight: 0.0020 chunk 225 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 391 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN D 130 GLN E 487 ASN E 935 GLN F 907 ASN F1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.219854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.134832 restraints weight = 39515.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.137105 restraints weight = 22977.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.135583 restraints weight = 15011.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.136300 restraints weight = 15566.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.137081 restraints weight = 14148.875| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33146 Z= 0.134 Angle : 0.576 12.171 45224 Z= 0.289 Chirality : 0.045 0.423 5232 Planarity : 0.004 0.059 5767 Dihedral : 5.704 54.549 5152 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.80 % Allowed : 19.95 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.30 (0.13), residues: 4062 helix: 1.62 (0.20), residues: 680 sheet: -0.03 (0.16), residues: 1063 loop : -0.83 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 68 TYR 0.024 0.001 TYR D 51 PHE 0.024 0.001 PHE A 429 TRP 0.011 0.001 TRP F 353 HIS 0.003 0.001 HIS E 655 Details of bonding type rmsd covalent geometry : bond 0.00318 (33087) covalent geometry : angle 0.55856 (45070) SS BOND : bond 0.00275 ( 23) SS BOND : angle 1.29417 ( 46) hydrogen bonds : bond 0.03548 ( 1249) hydrogen bonds : angle 5.44294 ( 3492) link_BETA1-4 : bond 0.00326 ( 4) link_BETA1-4 : angle 2.07669 ( 12) link_NAG-ASN : bond 0.00795 ( 32) link_NAG-ASN : angle 2.88705 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 526 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8194 (t80) cc_final: 0.7980 (t80) REVERT: A 191 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: A 280 ASN cc_start: 0.8166 (t0) cc_final: 0.7839 (t0) REVERT: A 347 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6550 (t80) REVERT: A 378 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7360 (ttmm) REVERT: A 740 MET cc_start: 0.7800 (tpp) cc_final: 0.7487 (tpp) REVERT: A 794 ILE cc_start: 0.7979 (mt) cc_final: 0.7499 (tt) REVERT: A 796 ASP cc_start: 0.7981 (t0) cc_final: 0.7529 (m-30) REVERT: A 821 LEU cc_start: 0.8690 (tp) cc_final: 0.8457 (tt) REVERT: A 823 PHE cc_start: 0.7778 (t80) cc_final: 0.7544 (t80) REVERT: A 864 LEU cc_start: 0.8730 (tt) cc_final: 0.8424 (tt) REVERT: A 935 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: A 979 ASP cc_start: 0.7447 (t0) cc_final: 0.7146 (t0) REVERT: C 177 GLN cc_start: 0.7847 (mp-120) cc_final: 0.7642 (mp10) REVERT: C 205 ASN cc_start: 0.8859 (t0) cc_final: 0.8548 (t0) REVERT: C 215 LYS cc_start: 0.8387 (tppt) cc_final: 0.7654 (mtmt) REVERT: D 49 MET cc_start: 0.7300 (mmt) cc_final: 0.7054 (mmt) REVERT: E 58 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: E 280 ASN cc_start: 0.7883 (t0) cc_final: 0.7638 (t0) REVERT: E 318 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7673 (p90) REVERT: E 531 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8467 (p) REVERT: E 619 GLU cc_start: 0.8106 (mp0) cc_final: 0.7785 (mp0) REVERT: E 737 ASP cc_start: 0.7768 (p0) cc_final: 0.7340 (p0) REVERT: E 1126 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7838 (p) REVERT: E 1139 ASP cc_start: 0.8092 (t0) cc_final: 0.7873 (t0) REVERT: F 53 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: F 206 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8088 (ttmt) REVERT: F 221 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.8009 (m) REVERT: F 239 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: F 274 THR cc_start: 0.7315 (m) cc_final: 0.6882 (p) REVERT: F 298 GLU cc_start: 0.7718 (tt0) cc_final: 0.7498 (tt0) REVERT: F 319 ARG cc_start: 0.7412 (ptp-110) cc_final: 0.7004 (ptp-110) REVERT: F 357 ARG cc_start: 0.7904 (ptm-80) cc_final: 0.7665 (ttp80) REVERT: F 390 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8591 (mm) REVERT: F 558 LYS cc_start: 0.8962 (pttp) cc_final: 0.8610 (pttm) REVERT: F 588 THR cc_start: 0.8799 (m) cc_final: 0.8456 (p) REVERT: F 823 PHE cc_start: 0.7676 (t80) cc_final: 0.7379 (m-80) REVERT: F 978 ASN cc_start: 0.8498 (t0) cc_final: 0.8184 (t0) REVERT: F 1084 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: H 5 LYS cc_start: 0.5256 (tmtt) cc_final: 0.5020 (tmtt) REVERT: H 40 ARG cc_start: 0.7391 (ptt180) cc_final: 0.7093 (ptt90) REVERT: H 59 LYS cc_start: 0.8057 (mttt) cc_final: 0.7761 (mttt) REVERT: H 111 GLN cc_start: 0.6276 (tp-100) cc_final: 0.5492 (mt0) REVERT: J 49 MET cc_start: 0.7305 (mmt) cc_final: 0.6941 (mmt) REVERT: J 72 MET cc_start: 0.4910 (mmp) cc_final: 0.4422 (mmp) outliers start: 172 outliers final: 123 residues processed: 645 average time/residue: 0.1606 time to fit residues: 177.2917 Evaluate side-chains 627 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 492 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 982 SER Chi-restraints excluded: chain E residue 1008 VAL Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1126 CYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 392 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 907 ASN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 93 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 283 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 169 optimal weight: 0.2980 chunk 46 optimal weight: 30.0000 chunk 305 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN D 130 GLN E 895 GLN E 907 ASN F 360 ASN F 450 ASN F1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.219471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.129737 restraints weight = 39731.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.134948 restraints weight = 22640.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.136516 restraints weight = 14395.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.137019 restraints weight = 11591.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.137428 restraints weight = 12199.481| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33146 Z= 0.150 Angle : 0.584 11.569 45224 Z= 0.292 Chirality : 0.045 0.410 5232 Planarity : 0.004 0.059 5767 Dihedral : 5.650 54.564 5150 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.80 % Allowed : 20.06 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.28 (0.13), residues: 4062 helix: 1.64 (0.20), residues: 681 sheet: -0.01 (0.16), residues: 1044 loop : -0.82 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 68 TYR 0.024 0.001 TYR D 51 PHE 0.016 0.001 PHE E 898 TRP 0.011 0.001 TRP F 64 HIS 0.003 0.001 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00357 (33087) covalent geometry : angle 0.56743 (45070) SS BOND : bond 0.00295 ( 23) SS BOND : angle 1.32106 ( 46) hydrogen bonds : bond 0.03547 ( 1249) hydrogen bonds : angle 5.39409 ( 3492) link_BETA1-4 : bond 0.00345 ( 4) link_BETA1-4 : angle 2.07765 ( 12) link_NAG-ASN : bond 0.00801 ( 32) link_NAG-ASN : angle 2.83463 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 500 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8151 (t80) cc_final: 0.7937 (t80) REVERT: A 92 PHE cc_start: 0.8268 (t80) cc_final: 0.8026 (t80) REVERT: A 191 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: A 280 ASN cc_start: 0.8204 (t0) cc_final: 0.7863 (t0) REVERT: A 289 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (p) REVERT: A 347 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6498 (t80) REVERT: A 378 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7337 (ttmm) REVERT: A 535 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8601 (mmtm) REVERT: A 794 ILE cc_start: 0.8002 (mt) cc_final: 0.7524 (tt) REVERT: A 796 ASP cc_start: 0.7949 (t0) cc_final: 0.7517 (m-30) REVERT: A 821 LEU cc_start: 0.8744 (tp) cc_final: 0.8440 (tt) REVERT: A 823 PHE cc_start: 0.7791 (t80) cc_final: 0.7555 (t80) REVERT: A 918 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 931 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 935 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: A 979 ASP cc_start: 0.7483 (t0) cc_final: 0.7192 (t0) REVERT: C 177 GLN cc_start: 0.7873 (mp-120) cc_final: 0.7646 (mp10) REVERT: C 205 ASN cc_start: 0.8880 (t0) cc_final: 0.8546 (t0) REVERT: C 215 LYS cc_start: 0.8385 (tppt) cc_final: 0.7648 (mtmt) REVERT: D 208 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8021 (tptp) REVERT: E 58 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: E 318 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7755 (p90) REVERT: E 531 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8505 (p) REVERT: E 619 GLU cc_start: 0.8150 (mp0) cc_final: 0.7900 (mp0) REVERT: F 53 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: F 206 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8358 (ttmt) REVERT: F 221 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7995 (m) REVERT: F 239 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: F 274 THR cc_start: 0.7304 (m) cc_final: 0.6866 (p) REVERT: F 298 GLU cc_start: 0.7726 (tt0) cc_final: 0.7504 (tt0) REVERT: F 357 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7618 (ttp80) REVERT: F 390 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8600 (mm) REVERT: F 529 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8411 (mtmm) REVERT: F 558 LYS cc_start: 0.8949 (pttp) cc_final: 0.8613 (pttm) REVERT: F 588 THR cc_start: 0.8806 (m) cc_final: 0.8450 (p) REVERT: F 823 PHE cc_start: 0.7689 (t80) cc_final: 0.7401 (m-80) REVERT: F 957 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7153 (mt0) REVERT: F 978 ASN cc_start: 0.8506 (t0) cc_final: 0.8184 (t0) REVERT: F 1084 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: H 40 ARG cc_start: 0.7379 (ptt180) cc_final: 0.7079 (ptt90) REVERT: H 68 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8067 (mtp-110) REVERT: H 135 LYS cc_start: 0.7379 (mmtt) cc_final: 0.7123 (mmtm) REVERT: H 165 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6084 (pp) REVERT: J 49 MET cc_start: 0.7273 (mmt) cc_final: 0.6776 (mmt) REVERT: J 72 MET cc_start: 0.4886 (mmp) cc_final: 0.4373 (mmp) outliers start: 172 outliers final: 131 residues processed: 620 average time/residue: 0.1597 time to fit residues: 168.8268 Evaluate side-chains 628 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 481 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 982 SER Chi-restraints excluded: chain E residue 1003 SER Chi-restraints excluded: chain E residue 1008 VAL Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1082 CYS Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 957 GLN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 223 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 361 optimal weight: 0.3980 chunk 256 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN A1036 GLN D 130 GLN E 907 ASN E1106 GLN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.219930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.129846 restraints weight = 39791.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.134975 restraints weight = 22666.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.136218 restraints weight = 13264.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.137302 restraints weight = 12402.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.137340 restraints weight = 12627.200| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33146 Z= 0.123 Angle : 0.578 11.989 45224 Z= 0.288 Chirality : 0.045 0.354 5232 Planarity : 0.004 0.057 5767 Dihedral : 5.546 54.563 5150 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.44 % Allowed : 20.42 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.23 (0.13), residues: 4062 helix: 1.73 (0.20), residues: 678 sheet: 0.04 (0.16), residues: 1043 loop : -0.81 (0.13), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 68 TYR 0.022 0.001 TYR D 51 PHE 0.025 0.001 PHE A 429 TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00290 (33087) covalent geometry : angle 0.56222 (45070) SS BOND : bond 0.00335 ( 23) SS BOND : angle 1.33840 ( 46) hydrogen bonds : bond 0.03404 ( 1249) hydrogen bonds : angle 5.30581 ( 3492) link_BETA1-4 : bond 0.00374 ( 4) link_BETA1-4 : angle 2.02348 ( 12) link_NAG-ASN : bond 0.00704 ( 32) link_NAG-ASN : angle 2.71844 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 500 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8118 (t80) cc_final: 0.7916 (t80) REVERT: A 92 PHE cc_start: 0.8296 (t80) cc_final: 0.8047 (t80) REVERT: A 191 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 280 ASN cc_start: 0.8217 (t0) cc_final: 0.7921 (t0) REVERT: A 289 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 347 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6493 (t80) REVERT: A 378 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7367 (ttmm) REVERT: A 726 ILE cc_start: 0.9242 (mp) cc_final: 0.8994 (mm) REVERT: A 794 ILE cc_start: 0.7976 (mt) cc_final: 0.7490 (tt) REVERT: A 796 ASP cc_start: 0.7938 (t0) cc_final: 0.7542 (m-30) REVERT: A 823 PHE cc_start: 0.7809 (t80) cc_final: 0.7599 (t80) REVERT: A 864 LEU cc_start: 0.8736 (tp) cc_final: 0.8263 (tt) REVERT: A 931 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (tt) REVERT: A 935 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: A 979 ASP cc_start: 0.7439 (t0) cc_final: 0.7185 (t0) REVERT: A 1101 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.6887 (p-80) REVERT: C 215 LYS cc_start: 0.8304 (tppt) cc_final: 0.7640 (mtmt) REVERT: D 49 MET cc_start: 0.7390 (mmt) cc_final: 0.7002 (mtt) REVERT: D 208 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7955 (tptp) REVERT: E 58 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: E 280 ASN cc_start: 0.7925 (t0) cc_final: 0.7674 (t0) REVERT: E 318 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7645 (p90) REVERT: E 531 THR cc_start: 0.8905 (m) cc_final: 0.8549 (p) REVERT: E 619 GLU cc_start: 0.8189 (mp0) cc_final: 0.7934 (mp0) REVERT: E 787 GLN cc_start: 0.8311 (pt0) cc_final: 0.8025 (pt0) REVERT: F 53 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: F 221 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7959 (m) REVERT: F 239 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: F 298 GLU cc_start: 0.7691 (tt0) cc_final: 0.7471 (tt0) REVERT: F 357 ARG cc_start: 0.7936 (ptm-80) cc_final: 0.7688 (ttp80) REVERT: F 390 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8607 (mm) REVERT: F 529 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8401 (mtmm) REVERT: F 558 LYS cc_start: 0.8946 (pttp) cc_final: 0.8608 (pttm) REVERT: F 588 THR cc_start: 0.8823 (m) cc_final: 0.8498 (p) REVERT: F 823 PHE cc_start: 0.7649 (t80) cc_final: 0.7381 (m-80) REVERT: F 918 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7158 (mp0) REVERT: F 957 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: F 978 ASN cc_start: 0.8478 (t0) cc_final: 0.8172 (t0) REVERT: F 1084 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: H 38 TRP cc_start: 0.6795 (m100) cc_final: 0.6327 (m100) REVERT: H 40 ARG cc_start: 0.7368 (ptt180) cc_final: 0.7070 (ptt90) REVERT: H 135 LYS cc_start: 0.7388 (mmtt) cc_final: 0.7185 (mmtm) REVERT: J 33 ASN cc_start: 0.8012 (m-40) cc_final: 0.7773 (t0) REVERT: J 49 MET cc_start: 0.7209 (mmt) cc_final: 0.6722 (mmt) REVERT: J 72 MET cc_start: 0.4885 (mmp) cc_final: 0.4368 (mmp) outliers start: 159 outliers final: 122 residues processed: 611 average time/residue: 0.1586 time to fit residues: 165.3440 Evaluate side-chains 621 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 485 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 632 THR Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 982 SER Chi-restraints excluded: chain E residue 1003 SER Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1082 CYS Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 957 GLN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 58 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 313 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 114 optimal weight: 0.1980 chunk 315 optimal weight: 0.7980 chunk 285 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 209 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN E 703 ASN E 907 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 907 ASN J 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.230259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.143525 restraints weight = 39862.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.147245 restraints weight = 21630.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.147651 restraints weight = 12352.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.148613 restraints weight = 12382.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.148758 restraints weight = 11151.257| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33146 Z= 0.130 Angle : 0.586 12.387 45224 Z= 0.291 Chirality : 0.045 0.348 5232 Planarity : 0.004 0.059 5767 Dihedral : 5.504 54.711 5149 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.13 % Allowed : 21.21 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.20 (0.13), residues: 4062 helix: 1.69 (0.20), residues: 687 sheet: 0.07 (0.16), residues: 1048 loop : -0.79 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 68 TYR 0.022 0.001 TYR D 51 PHE 0.015 0.001 PHE A 898 TRP 0.012 0.001 TRP F 64 HIS 0.003 0.001 HIS J 40 Details of bonding type rmsd covalent geometry : bond 0.00309 (33087) covalent geometry : angle 0.57167 (45070) SS BOND : bond 0.00287 ( 23) SS BOND : angle 1.27366 ( 46) hydrogen bonds : bond 0.03417 ( 1249) hydrogen bonds : angle 5.28356 ( 3492) link_BETA1-4 : bond 0.00363 ( 4) link_BETA1-4 : angle 2.00620 ( 12) link_NAG-ASN : bond 0.00778 ( 32) link_NAG-ASN : angle 2.66637 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 490 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8151 (t80) cc_final: 0.7951 (t80) REVERT: A 92 PHE cc_start: 0.8308 (t80) cc_final: 0.8064 (t80) REVERT: A 191 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 280 ASN cc_start: 0.8233 (t0) cc_final: 0.7948 (t0) REVERT: A 289 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 378 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7364 (ttmm) REVERT: A 380 TYR cc_start: 0.8839 (m-80) cc_final: 0.7998 (m-80) REVERT: A 726 ILE cc_start: 0.9223 (mp) cc_final: 0.8978 (mm) REVERT: A 740 MET cc_start: 0.7753 (tpp) cc_final: 0.7440 (mmt) REVERT: A 794 ILE cc_start: 0.8003 (mt) cc_final: 0.7534 (tt) REVERT: A 796 ASP cc_start: 0.7922 (t0) cc_final: 0.7536 (m-30) REVERT: A 864 LEU cc_start: 0.8787 (tp) cc_final: 0.8305 (tt) REVERT: A 931 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8616 (tt) REVERT: A 979 ASP cc_start: 0.7408 (t0) cc_final: 0.7166 (t0) REVERT: A 1101 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.6879 (p-80) REVERT: D 49 MET cc_start: 0.7369 (mmt) cc_final: 0.6966 (mtt) REVERT: D 208 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7949 (tptp) REVERT: E 58 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: E 318 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7664 (p90) REVERT: E 531 THR cc_start: 0.8877 (m) cc_final: 0.8500 (p) REVERT: E 619 GLU cc_start: 0.8208 (mp0) cc_final: 0.7962 (mp0) REVERT: E 703 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.7897 (p0) REVERT: E 787 GLN cc_start: 0.8314 (pt0) cc_final: 0.8029 (pt0) REVERT: F 53 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: F 206 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8299 (ttmt) REVERT: F 221 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7885 (m) REVERT: F 239 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: F 274 THR cc_start: 0.7304 (m) cc_final: 0.6901 (p) REVERT: F 298 GLU cc_start: 0.7673 (tt0) cc_final: 0.7464 (tt0) REVERT: F 357 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7695 (ttp80) REVERT: F 390 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8592 (mm) REVERT: F 493 GLN cc_start: 0.7986 (tp40) cc_final: 0.7710 (tm-30) REVERT: F 529 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8423 (mtmm) REVERT: F 532 ASN cc_start: 0.8327 (m-40) cc_final: 0.7924 (p0) REVERT: F 558 LYS cc_start: 0.8878 (pttp) cc_final: 0.8533 (pttm) REVERT: F 823 PHE cc_start: 0.7626 (t80) cc_final: 0.7399 (m-80) REVERT: F 957 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: F 978 ASN cc_start: 0.8422 (t0) cc_final: 0.8128 (t0) REVERT: F 1084 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: H 38 TRP cc_start: 0.6801 (m100) cc_final: 0.6366 (m100) REVERT: H 40 ARG cc_start: 0.7383 (ptt180) cc_final: 0.7122 (ptt90) REVERT: H 68 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8098 (mtp-110) REVERT: H 135 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7190 (mmtm) REVERT: H 165 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6117 (pp) REVERT: J 49 MET cc_start: 0.7162 (mmt) cc_final: 0.6685 (mmt) REVERT: J 72 MET cc_start: 0.4864 (mmp) cc_final: 0.4291 (mmt) outliers start: 148 outliers final: 117 residues processed: 593 average time/residue: 0.1562 time to fit residues: 158.8844 Evaluate side-chains 611 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 480 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 703 ASN Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 982 SER Chi-restraints excluded: chain E residue 1003 SER Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 957 GLN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 144 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 376 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN E 703 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.229983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.143302 restraints weight = 40015.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.147863 restraints weight = 22051.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.148044 restraints weight = 13177.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.148709 restraints weight = 11708.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.149524 restraints weight = 11928.572| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 33146 Z= 0.175 Angle : 0.742 59.049 45224 Z= 0.406 Chirality : 0.052 1.749 5232 Planarity : 0.005 0.194 5767 Dihedral : 5.506 54.717 5148 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.79 % Allowed : 21.48 % Favored : 74.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.20 (0.13), residues: 4062 helix: 1.68 (0.20), residues: 687 sheet: 0.08 (0.16), residues: 1055 loop : -0.79 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 68 TYR 0.050 0.001 TYR F 660 PHE 0.014 0.001 PHE A 898 TRP 0.015 0.001 TRP A 64 HIS 0.272 0.004 HIS J 40 Details of bonding type rmsd covalent geometry : bond 0.00401 (33087) covalent geometry : angle 0.72843 (45070) SS BOND : bond 0.00286 ( 23) SS BOND : angle 1.28414 ( 46) hydrogen bonds : bond 0.03492 ( 1249) hydrogen bonds : angle 5.29465 ( 3492) link_BETA1-4 : bond 0.00290 ( 4) link_BETA1-4 : angle 2.04690 ( 12) link_NAG-ASN : bond 0.01011 ( 32) link_NAG-ASN : angle 3.01667 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 482 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8180 (t80) cc_final: 0.7975 (t80) REVERT: A 92 PHE cc_start: 0.8193 (t80) cc_final: 0.7946 (t80) REVERT: A 191 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: A 280 ASN cc_start: 0.8225 (t0) cc_final: 0.7932 (t0) REVERT: A 289 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 378 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7240 (ttmm) REVERT: A 380 TYR cc_start: 0.8771 (m-80) cc_final: 0.7935 (m-80) REVERT: A 726 ILE cc_start: 0.9232 (mp) cc_final: 0.8996 (mm) REVERT: A 740 MET cc_start: 0.7806 (tpp) cc_final: 0.7483 (mmt) REVERT: A 794 ILE cc_start: 0.8003 (mt) cc_final: 0.7521 (tt) REVERT: A 796 ASP cc_start: 0.7919 (t0) cc_final: 0.7519 (m-30) REVERT: A 864 LEU cc_start: 0.8757 (tp) cc_final: 0.8300 (tt) REVERT: A 931 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8612 (tt) REVERT: A 935 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: A 979 ASP cc_start: 0.7483 (t0) cc_final: 0.7218 (t0) REVERT: A 1101 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.6901 (p-80) REVERT: D 49 MET cc_start: 0.7374 (mmt) cc_final: 0.6949 (mtt) REVERT: D 208 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7890 (tptp) REVERT: E 58 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: E 318 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7658 (p90) REVERT: E 531 THR cc_start: 0.8844 (m) cc_final: 0.8433 (p) REVERT: E 619 GLU cc_start: 0.8261 (mp0) cc_final: 0.7984 (mp0) REVERT: E 787 GLN cc_start: 0.8327 (pt0) cc_final: 0.8035 (pt0) REVERT: F 53 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: F 206 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8230 (ttmt) REVERT: F 221 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7825 (m) REVERT: F 239 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: F 274 THR cc_start: 0.7231 (m) cc_final: 0.6834 (p) REVERT: F 298 GLU cc_start: 0.7676 (tt0) cc_final: 0.7466 (tt0) REVERT: F 357 ARG cc_start: 0.7943 (ptm-80) cc_final: 0.7707 (ttp80) REVERT: F 390 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8572 (mm) REVERT: F 493 GLN cc_start: 0.7954 (tp40) cc_final: 0.7600 (tm-30) REVERT: F 529 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8416 (mtmm) REVERT: F 532 ASN cc_start: 0.8338 (m-40) cc_final: 0.7923 (p0) REVERT: F 558 LYS cc_start: 0.8900 (pttp) cc_final: 0.8548 (pttm) REVERT: F 787 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: F 823 PHE cc_start: 0.7634 (t80) cc_final: 0.7379 (m-80) REVERT: F 957 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: F 978 ASN cc_start: 0.8450 (t0) cc_final: 0.8141 (t0) REVERT: F 1084 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: H 40 ARG cc_start: 0.7400 (ptt180) cc_final: 0.7082 (ptt90) REVERT: H 68 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8193 (mtp-110) REVERT: H 165 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.5996 (pp) REVERT: J 40 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.7010 (t70) REVERT: J 49 MET cc_start: 0.7304 (mmt) cc_final: 0.6745 (mmt) REVERT: J 72 MET cc_start: 0.4805 (mmp) cc_final: 0.4235 (mmt) outliers start: 136 outliers final: 119 residues processed: 578 average time/residue: 0.1554 time to fit residues: 153.8981 Evaluate side-chains 616 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 481 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 711 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 982 SER Chi-restraints excluded: chain E residue 1003 SER Chi-restraints excluded: chain E residue 1008 VAL Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1105 THR Chi-restraints excluded: chain E residue 1115 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 957 GLN Chi-restraints excluded: chain F residue 977 LEU Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1098 ASN Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 49 TRP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 192 SER Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 40 HIS Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 71 optimal weight: 0.6980 chunk 286 optimal weight: 0.1980 chunk 252 optimal weight: 0.4980 chunk 283 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 300 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN D 201 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 GLN ** F 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.231708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.144180 restraints weight = 39987.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148614 restraints weight = 21478.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.150167 restraints weight = 13520.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.150712 restraints weight = 11550.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.151289 restraints weight = 11872.757| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33146 Z= 0.134 Angle : 0.588 12.374 45224 Z= 0.292 Chirality : 0.045 0.343 5232 Planarity : 0.004 0.062 5767 Dihedral : 5.486 54.746 5148 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.99 % Allowed : 21.21 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 aren not related in a simple way. whole: -0.18 (0.13), residues: 4062 helix: 1.72 (0.20), residues: 687 sheet: 0.09 (0.16), residues: 1055 loop : -0.78 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 68 TYR 0.028 0.001 TYR A 266 PHE 0.015 0.001 PHE A 898 TRP 0.021 0.001 TRP A 64 HIS 0.005 0.001 HIS J 40 Details of bonding type rmsd covalent geometry : bond 0.00318 (33087) covalent geometry : angle 0.57404 (45070) SS BOND : bond 0.00287 ( 23) SS BOND : angle 1.26829 ( 46) hydrogen bonds : bond 0.03416 ( 1249) hydrogen bonds : angle 5.28157 ( 3492) link_BETA1-4 : bond 0.00340 ( 4) link_BETA1-4 : angle 1.99388 ( 12) link_NAG-ASN : bond 0.00913 ( 32) link_NAG-ASN : angle 2.64212 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6149.38 seconds wall clock time: 106 minutes 55.58 seconds (6415.58 seconds total)