Starting phenix.real_space_refine on Thu May 29 19:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gdr_29950/05_2025/8gdr_29950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gdr_29950/05_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_29950/05_2025/8gdr_29950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gdr_29950/05_2025/8gdr_29950.map" model { file = "/net/cci-nas-00/data/ceres_data/8gdr_29950/05_2025/8gdr_29950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gdr_29950/05_2025/8gdr_29950.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.08, per 1000 atoms: 0.59 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: 8.74 Conformation dependent library (CDL) restraints added in 4.5 seconds 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: 5.70 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: 19.53 Time building geometry restraints manager: 10.13 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: 4.090 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: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.270 Set scattering table: 0.310 Process input model: 81.920 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP H 49 HIS 0.007 0.001 HIS C 206 PHE 0.025 0.001 PHE E 562 TYR 0.017 0.001 TYR D 51 ARG 0.010 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.09082 ( 32) link_NAG-ASN : angle 4.11673 ( 96) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 3.06390 ( 12) hydrogen bonds : bond 0.12274 ( 1249) hydrogen bonds : angle 7.60007 ( 3492) SS BOND : bond 0.00446 ( 23) SS BOND : angle 1.07221 ( 46) covalent geometry : bond 0.00369 (33087) covalent geometry : angle 0.56749 (45070) *********************** 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 : 3.261 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 909 ILE cc_start: 0.9050 (pt) cc_final: 0.8767 (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: 0.6939 (tm-30) REVERT: E 531 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8327 (p) REVERT: E 869 MET cc_start: 0.8791 (mtp) cc_final: 0.8500 (mtp) REVERT: E 1126 CYS cc_start: 0.8623 (m) cc_final: 0.8070 (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: 0.7871 (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: 0.5181 (pt0) REVERT: J 44 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6614 (mmmt) outliers start: 17 outliers final: 11 residues processed: 536 average time/residue: 0.4010 time to fit residues: 358.2453 Evaluate side-chains 515 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 503 time to evaluate : 3.586 ------------------------------------------------------------------------------- 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 805 ILE 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 342 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 105 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 368 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 164 ASN 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 907 ASN E 920 GLN E 955 ASN E 969 ASN E1088 HIS F 66 HIS 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 = 0.4238 r_free = 0.4238 target = 0.216586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128137 restraints weight = 39653.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.131448 restraints weight = 23589.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.131356 restraints weight = 14365.328| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33146 Z= 0.216 Angle : 0.661 19.735 45224 Z= 0.332 Chirality : 0.049 0.632 5232 Planarity : 0.005 0.071 5767 Dihedral : 6.678 59.084 5166 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.05 % Allowed : 17.58 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4062 helix: 1.23 (0.20), residues: 667 sheet: -0.34 (0.15), residues: 1090 loop : -0.96 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 189 HIS 0.006 0.001 HIS E 655 PHE 0.022 0.002 PHE A 168 TYR 0.029 0.001 TYR D 51 ARG 0.006 0.001 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 32) link_NAG-ASN : angle 3.94533 ( 96) link_BETA1-4 : bond 0.00573 ( 4) link_BETA1-4 : angle 2.47577 ( 12) hydrogen bonds : bond 0.04348 ( 1249) hydrogen bonds : angle 6.08931 ( 3492) SS BOND : bond 0.00398 ( 23) SS BOND : angle 1.54073 ( 46) covalent geometry : bond 0.00513 (33087) covalent geometry : angle 0.63333 (45070) *********************** 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 684 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 539 time to evaluate : 3.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: A 380 TYR cc_start: 0.8562 (m-80) cc_final: 0.8291 (m-80) REVERT: A 740 MET cc_start: 0.8058 (tpp) cc_final: 0.7786 (mmt) REVERT: A 931 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 935 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: A 979 ASP cc_start: 0.7377 (t0) cc_final: 0.7161 (t0) REVERT: A 1074 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8299 (p0) REVERT: C 89 PRO cc_start: 0.8969 (Cg_exo) cc_final: 0.8715 (Cg_endo) REVERT: C 205 ASN cc_start: 0.9009 (t0) cc_final: 0.8494 (t0) REVERT: C 215 LYS cc_start: 0.8393 (tppt) cc_final: 0.7833 (ttmt) REVERT: D 49 MET cc_start: 0.7483 (mmt) cc_final: 0.7169 (mmt) REVERT: E 34 ARG cc_start: 0.8809 (mmp80) cc_final: 0.8029 (tpp-160) REVERT: E 58 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: E 531 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8313 (p) REVERT: E 619 GLU cc_start: 0.7993 (mp0) cc_final: 0.7737 (mp0) REVERT: E 737 ASP cc_start: 0.7912 (p0) cc_final: 0.7545 (p0) REVERT: E 748 GLU cc_start: 0.7662 (pm20) cc_final: 0.7371 (pm20) REVERT: F 129 LYS cc_start: 0.7725 (mtpt) cc_final: 0.7212 (mmtt) REVERT: F 206 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8029 (ttmt) REVERT: F 269 TYR cc_start: 0.8191 (m-80) cc_final: 0.7390 (m-80) REVERT: F 357 ARG cc_start: 0.7921 (ptm-80) cc_final: 0.7690 (ttp80) REVERT: F 364 ASP cc_start: 0.8870 (t0) cc_final: 0.8622 (t0) REVERT: F 558 LYS cc_start: 0.8932 (pttp) cc_final: 0.8582 (pttm) REVERT: F 718 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8841 (p90) REVERT: F 767 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8620 (mt) REVERT: F 978 ASN cc_start: 0.8688 (t0) cc_final: 0.8300 (t0) REVERT: F 985 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7512 (t70) REVERT: H 40 ARG cc_start: 0.7370 (ptt180) cc_final: 0.7061 (ptt90) REVERT: H 59 LYS cc_start: 0.8237 (mttt) cc_final: 0.7916 (mttt) REVERT: H 111 GLN cc_start: 0.5990 (tp-100) cc_final: 0.5099 (pt0) REVERT: J 41 HIS cc_start: 0.7600 (t70) cc_final: 0.7285 (t-170) REVERT: J 44 LYS cc_start: 0.6994 (mmmt) cc_final: 0.6567 (mmmt) REVERT: J 49 MET cc_start: 0.7339 (mmt) cc_final: 0.6989 (mmt) REVERT: J 175 LYS cc_start: 0.7617 (mmtm) cc_final: 0.7416 (mmtm) outliers start: 145 outliers final: 80 residues processed: 642 average time/residue: 0.3996 time to fit residues: 436.1213 Evaluate side-chains 582 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 493 time to evaluate : 3.286 ------------------------------------------------------------------------------- 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 307 THR 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 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 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 531 THR 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 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 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 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 555 SER Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 718 PHE 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 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 1 optimal weight: 5.9990 chunk 191 optimal weight: 0.0470 chunk 244 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 250 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 246 optimal weight: 0.5980 chunk 253 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 A1005 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN D 130 GLN E 30 ASN E 207 HIS E 907 ASN ** E1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 HIS F 992 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.218637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.128673 restraints weight = 39873.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.133305 restraints weight = 23488.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.134819 restraints weight = 14176.369| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33146 Z= 0.130 Angle : 0.593 13.748 45224 Z= 0.298 Chirality : 0.046 0.387 5232 Planarity : 0.004 0.058 5767 Dihedral : 6.178 55.751 5157 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.91 % Allowed : 18.28 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4062 helix: 1.60 (0.20), residues: 669 sheet: -0.20 (0.16), residues: 1061 loop : -0.87 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 189 HIS 0.006 0.001 HIS E 207 PHE 0.023 0.001 PHE A 168 TYR 0.022 0.001 TYR D 51 ARG 0.008 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 32) link_NAG-ASN : angle 3.20584 ( 96) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 2.21553 ( 12) hydrogen bonds : bond 0.03802 ( 1249) hydrogen bonds : angle 5.76329 ( 3492) SS BOND : bond 0.00273 ( 23) SS BOND : angle 1.22056 ( 46) covalent geometry : bond 0.00300 (33087) covalent geometry : angle 0.57233 (45070) *********************** 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 676 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 536 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8293 (p) REVERT: A 347 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.6628 (t80) REVERT: A 378 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7182 (ttmm) REVERT: A 794 ILE cc_start: 0.7948 (mt) cc_final: 0.7438 (tt) REVERT: A 796 ASP cc_start: 0.8028 (t0) cc_final: 0.7535 (m-30) REVERT: A 821 LEU cc_start: 0.8783 (tp) cc_final: 0.8495 (tt) REVERT: A 909 ILE cc_start: 0.9110 (pt) cc_final: 0.8783 (pt) REVERT: A 918 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: A 935 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: A 979 ASP cc_start: 0.7387 (t0) cc_final: 0.7128 (t0) REVERT: C 89 PRO cc_start: 0.8883 (Cg_exo) cc_final: 0.8639 (Cg_endo) REVERT: C 205 ASN cc_start: 0.9019 (t0) cc_final: 0.8466 (t0) REVERT: C 215 LYS cc_start: 0.8408 (tppt) cc_final: 0.7640 (mtmt) REVERT: D 49 MET cc_start: 0.7356 (mmt) cc_final: 0.7045 (mmt) REVERT: E 58 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: E 318 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7841 (p90) REVERT: E 389 ASP cc_start: 0.8904 (p0) cc_final: 0.8587 (m-30) REVERT: E 509 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6667 (mtt90) REVERT: E 528 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7723 (ptpt) REVERT: E 531 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8312 (p) REVERT: E 737 ASP cc_start: 0.7803 (p0) cc_final: 0.7533 (p0) REVERT: E 740 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7745 (ttt) REVERT: E 787 GLN cc_start: 0.8281 (pt0) cc_final: 0.8015 (pt0) REVERT: F 94 SER cc_start: 0.8308 (t) cc_final: 0.8055 (m) REVERT: F 409 GLN cc_start: 0.8798 (mt0) cc_final: 0.7906 (tt0) REVERT: F 414 GLN cc_start: 0.8294 (tp40) cc_final: 0.7974 (tm-30) REVERT: F 558 LYS cc_start: 0.8937 (pttp) cc_final: 0.8616 (pttm) REVERT: F 588 THR cc_start: 0.8734 (m) cc_final: 0.8321 (p) REVERT: F 697 MET cc_start: 0.8344 (ttm) cc_final: 0.8129 (ttm) REVERT: F 767 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8543 (mt) REVERT: F 823 PHE cc_start: 0.7681 (t80) cc_final: 0.7170 (m-80) REVERT: F 978 ASN cc_start: 0.8624 (t0) cc_final: 0.8257 (t0) REVERT: F 1084 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: H 4 LEU cc_start: 0.6785 (tp) cc_final: 0.6571 (tp) REVERT: H 5 LYS cc_start: 0.4916 (tmtt) cc_final: 0.4663 (tmtt) REVERT: H 40 ARG cc_start: 0.7339 (ptt180) cc_final: 0.7068 (ptt90) REVERT: H 111 GLN cc_start: 0.5996 (tp-100) cc_final: 0.5153 (pt0) REVERT: H 135 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7328 (mmtm) REVERT: J 44 LYS cc_start: 0.7007 (mmmt) cc_final: 0.6802 (mmmt) REVERT: J 49 MET cc_start: 0.7318 (mmt) cc_final: 0.6916 (mmt) REVERT: J 72 MET cc_start: 0.4984 (mmp) cc_final: 0.4617 (mmp) outliers start: 140 outliers final: 85 residues processed: 625 average time/residue: 0.3755 time to fit residues: 395.3072 Evaluate side-chains 599 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 504 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 205 SER 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 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 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 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 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 318 PHE 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 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 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain F residue 33 THR 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 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 73 LYS 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 75 optimal weight: 0.0470 chunk 210 optimal weight: 9.9990 chunk 361 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 387 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.8682 ------------------------------------------------------------------------------- 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 544 ASN A 955 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN D 130 GLN D 171 GLN D 188 GLN E 907 ASN E 935 GLN E1119 ASN F 360 ASN F 613 GLN F1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.217218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125766 restraints weight = 39717.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.130882 restraints weight = 21403.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.134143 restraints weight = 13701.263| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33146 Z= 0.166 Angle : 0.595 12.304 45224 Z= 0.299 Chirality : 0.046 0.424 5232 Planarity : 0.004 0.059 5767 Dihedral : 6.040 56.743 5156 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.38 % Allowed : 18.75 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4062 helix: 1.61 (0.20), residues: 669 sheet: -0.17 (0.16), residues: 1069 loop : -0.88 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 109 HIS 0.003 0.001 HIS E 655 PHE 0.027 0.001 PHE A 541 TYR 0.026 0.001 TYR D 51 ARG 0.005 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 32) link_NAG-ASN : angle 3.13713 ( 96) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 2.15222 ( 12) hydrogen bonds : bond 0.03793 ( 1249) hydrogen bonds : angle 5.64500 ( 3492) SS BOND : bond 0.00299 ( 23) SS BOND : angle 1.38069 ( 46) covalent geometry : bond 0.00396 (33087) covalent geometry : angle 0.57564 (45070) *********************** 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 673 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 516 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8260 (p) REVERT: A 347 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 378 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7253 (ttmm) REVERT: A 740 MET cc_start: 0.7874 (tpp) cc_final: 0.7602 (mmt) REVERT: A 794 ILE cc_start: 0.8036 (mt) cc_final: 0.7535 (tt) REVERT: A 796 ASP cc_start: 0.7998 (t0) cc_final: 0.7519 (m-30) REVERT: A 821 LEU cc_start: 0.8705 (tp) cc_final: 0.8365 (tt) REVERT: A 909 ILE cc_start: 0.9387 (pt) cc_final: 0.9072 (pt) REVERT: A 918 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 935 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: A 979 ASP cc_start: 0.7456 (t0) cc_final: 0.7170 (t0) REVERT: C 89 PRO cc_start: 0.8910 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: C 205 ASN cc_start: 0.8995 (t0) cc_final: 0.8414 (t0) REVERT: C 215 LYS cc_start: 0.8391 (tppt) cc_final: 0.7642 (mtmt) REVERT: E 34 ARG cc_start: 0.8786 (tpp-160) cc_final: 0.8446 (tpp80) REVERT: E 58 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: E 177 MET cc_start: 0.3432 (mmt) cc_final: 0.3216 (mmp) REVERT: E 221 SER cc_start: 0.9087 (t) cc_final: 0.8860 (m) REVERT: E 224 GLU cc_start: 0.7396 (mp0) cc_final: 0.7060 (mp0) REVERT: E 318 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7855 (p90) REVERT: E 509 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6804 (mtt90) REVERT: E 531 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8434 (p) REVERT: E 737 ASP cc_start: 0.7777 (p0) cc_final: 0.7442 (p0) REVERT: E 916 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8269 (tp) REVERT: E 988 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7694 (tm-30) REVERT: F 53 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: F 239 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: F 274 THR cc_start: 0.7371 (m) cc_final: 0.6932 (p) REVERT: F 390 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8631 (mm) REVERT: F 558 LYS cc_start: 0.8955 (pttp) cc_final: 0.8632 (pttm) REVERT: F 767 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (mt) REVERT: F 823 PHE cc_start: 0.7724 (t80) cc_final: 0.7327 (m-80) REVERT: F 978 ASN cc_start: 0.8572 (t0) cc_final: 0.8210 (t0) REVERT: F 1084 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: H 40 ARG cc_start: 0.7331 (ptt180) cc_final: 0.7062 (ptt90) REVERT: H 59 LYS cc_start: 0.8165 (mttt) cc_final: 0.7844 (mttt) REVERT: H 68 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8061 (mtp-110) REVERT: J 49 MET cc_start: 0.7268 (mmt) cc_final: 0.6931 (mmt) REVERT: J 72 MET cc_start: 0.4956 (mmp) cc_final: 0.4547 (mmp) outliers start: 157 outliers final: 113 residues processed: 623 average time/residue: 0.3792 time to fit residues: 398.8446 Evaluate side-chains 617 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 491 time to evaluate : 3.123 ------------------------------------------------------------------------------- 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 205 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 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 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 94 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 106 LYS Chi-restraints excluded: chain D residue 107 LEU 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 597 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 727 LEU 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 794 ILE Chi-restraints excluded: chain E residue 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 916 LEU 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 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 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 511 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 552 LEU 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 767 LEU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 884 SER 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 10 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 335 optimal weight: 0.9990 chunk 333 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 325 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 188 GLN D 201 HIS E 360 ASN E 703 ASN E 907 ASN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1010 GLN H 1 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.218824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.132086 restraints weight = 39586.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.133853 restraints weight = 24722.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.134829 restraints weight = 15513.776| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33146 Z= 0.158 Angle : 0.589 12.637 45224 Z= 0.294 Chirality : 0.045 0.368 5232 Planarity : 0.004 0.060 5767 Dihedral : 5.840 54.614 5154 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.97 % Allowed : 18.75 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4062 helix: 1.56 (0.20), residues: 675 sheet: -0.09 (0.16), residues: 1065 loop : -0.87 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.004 0.001 HIS J 40 PHE 0.023 0.001 PHE A 168 TYR 0.025 0.001 TYR D 51 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 32) link_NAG-ASN : angle 3.02529 ( 96) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 2.11493 ( 12) hydrogen bonds : bond 0.03717 ( 1249) hydrogen bonds : angle 5.55398 ( 3492) SS BOND : bond 0.00340 ( 23) SS BOND : angle 1.40471 ( 46) covalent geometry : bond 0.00376 (33087) covalent geometry : angle 0.57001 (45070) *********************** 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 685 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 507 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 314 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: A 347 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.6589 (t80) REVERT: A 378 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7197 (ttmm) REVERT: A 794 ILE cc_start: 0.7979 (mt) cc_final: 0.7462 (tt) REVERT: A 796 ASP cc_start: 0.7998 (t0) cc_final: 0.7509 (m-30) REVERT: A 821 LEU cc_start: 0.8655 (tp) cc_final: 0.8317 (tt) REVERT: A 909 ILE cc_start: 0.8964 (pt) cc_final: 0.8665 (pt) REVERT: A 918 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: A 935 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: A 979 ASP cc_start: 0.7483 (t0) cc_final: 0.7166 (t0) REVERT: C 177 GLN cc_start: 0.7907 (mp-120) cc_final: 0.7643 (mp10) REVERT: C 205 ASN cc_start: 0.9025 (t0) cc_final: 0.8450 (t0) REVERT: C 206 HIS cc_start: 0.6781 (t-90) cc_final: 0.6299 (t-90) REVERT: C 215 LYS cc_start: 0.8387 (tppt) cc_final: 0.7741 (mtmt) REVERT: D 49 MET cc_start: 0.7314 (mmt) cc_final: 0.7004 (mmt) REVERT: E 58 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: E 221 SER cc_start: 0.9035 (t) cc_final: 0.8768 (m) REVERT: E 318 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7868 (p90) REVERT: E 531 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8446 (p) REVERT: E 703 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7878 (p0) REVERT: E 740 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7861 (ttt) REVERT: E 916 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8241 (tp) REVERT: E 988 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7662 (tm-30) REVERT: F 53 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: F 239 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: F 319 ARG cc_start: 0.7451 (ptp-110) cc_final: 0.7231 (ptp-110) REVERT: F 390 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8621 (mm) REVERT: F 558 LYS cc_start: 0.8958 (pttp) cc_final: 0.8599 (pttm) REVERT: F 588 THR cc_start: 0.8771 (m) cc_final: 0.8410 (p) REVERT: F 767 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8594 (mt) REVERT: F 823 PHE cc_start: 0.7704 (t80) cc_final: 0.7294 (m-80) REVERT: F 957 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: F 978 ASN cc_start: 0.8523 (t0) cc_final: 0.8204 (t0) REVERT: F 1084 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: H 5 LYS cc_start: 0.5195 (tmtt) cc_final: 0.4987 (tmtt) REVERT: H 40 ARG cc_start: 0.7392 (ptt180) cc_final: 0.7101 (ptt90) REVERT: H 68 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8158 (mtp-110) REVERT: H 111 GLN cc_start: 0.6256 (tp-100) cc_final: 0.5396 (mt0) REVERT: H 135 LYS cc_start: 0.7396 (mmtt) cc_final: 0.7168 (mmtm) REVERT: J 49 MET cc_start: 0.7344 (mmt) cc_final: 0.6977 (mmt) REVERT: J 72 MET cc_start: 0.4952 (mmp) cc_final: 0.4477 (mmp) outliers start: 178 outliers final: 123 residues processed: 632 average time/residue: 0.3967 time to fit residues: 427.6675 Evaluate side-chains 631 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 491 time to evaluate : 3.567 ------------------------------------------------------------------------------- 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 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 306 PHE 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 752 LEU 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 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 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 D residue 18 ILE 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 105 THR 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 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 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 703 ASN 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 727 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 742 ILE Chi-restraints excluded: chain E residue 743 CYS 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 907 ASN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 982 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 E residue 1105 THR 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 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 552 LEU 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 767 LEU Chi-restraints excluded: chain F residue 805 ILE 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 1008 VAL Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1097 SER Chi-restraints excluded: chain F residue 1116 THR 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 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 239 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 391 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 355 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 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** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 487 ASN E 907 ASN E1048 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 762 GLN F1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.220591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.135089 restraints weight = 39852.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137816 restraints weight = 21764.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.136892 restraints weight = 13160.654| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1783 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 : 0.577 12.203 45224 Z= 0.289 Chirality : 0.045 0.442 5232 Planarity : 0.004 0.059 5767 Dihedral : 5.703 54.481 5152 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.97 % Allowed : 19.48 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4062 helix: 1.63 (0.20), residues: 674 sheet: -0.03 (0.16), residues: 1060 loop : -0.83 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 189 HIS 0.003 0.001 HIS E 655 PHE 0.024 0.001 PHE A 429 TYR 0.024 0.001 TYR D 51 ARG 0.009 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 32) link_NAG-ASN : angle 2.90455 ( 96) link_BETA1-4 : bond 0.00445 ( 4) link_BETA1-4 : angle 2.10297 ( 12) hydrogen bonds : bond 0.03574 ( 1249) hydrogen bonds : angle 5.46301 ( 3492) SS BOND : bond 0.00325 ( 23) SS BOND : angle 1.40391 ( 46) covalent geometry : bond 0.00316 (33087) covalent geometry : angle 0.55957 (45070) *********************** 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 685 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 507 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: A 314 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 347 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 794 ILE cc_start: 0.8005 (mt) cc_final: 0.7491 (tt) REVERT: A 796 ASP cc_start: 0.8033 (t0) cc_final: 0.7576 (m-30) REVERT: A 821 LEU cc_start: 0.8706 (tp) cc_final: 0.8422 (tt) REVERT: A 918 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 935 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: A 979 ASP cc_start: 0.7461 (t0) cc_final: 0.7168 (t0) REVERT: C 177 GLN cc_start: 0.7851 (mp-120) cc_final: 0.7635 (mp10) REVERT: C 215 LYS cc_start: 0.8384 (tppt) cc_final: 0.7652 (mtmt) REVERT: D 49 MET cc_start: 0.7399 (mmt) cc_final: 0.7133 (mmt) REVERT: E 58 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: E 221 SER cc_start: 0.9017 (t) cc_final: 0.8749 (m) REVERT: E 318 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7738 (p90) REVERT: E 531 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8478 (p) REVERT: E 740 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7863 (ttt) REVERT: E 916 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8190 (tp) REVERT: F 53 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: F 239 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: F 274 THR cc_start: 0.7332 (m) cc_final: 0.6904 (p) REVERT: F 314 GLN cc_start: 0.8525 (tt0) cc_final: 0.8163 (tp40) REVERT: F 357 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7923 (ttp80) REVERT: F 390 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8616 (mm) REVERT: F 493 GLN cc_start: 0.8040 (tp40) cc_final: 0.7723 (tm-30) REVERT: F 558 LYS cc_start: 0.8939 (pttp) cc_final: 0.8625 (pttm) REVERT: F 588 THR cc_start: 0.8793 (m) cc_final: 0.8455 (p) REVERT: F 823 PHE cc_start: 0.7672 (t80) cc_final: 0.7383 (m-80) REVERT: F 957 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: F 978 ASN cc_start: 0.8499 (t0) cc_final: 0.8183 (t0) REVERT: F 1084 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: H 5 LYS cc_start: 0.5166 (tmtt) cc_final: 0.4936 (tmtt) REVERT: H 40 ARG cc_start: 0.7408 (ptt180) cc_final: 0.7103 (ptt90) REVERT: H 111 GLN cc_start: 0.6182 (tp-100) cc_final: 0.5408 (mt0) REVERT: H 135 LYS cc_start: 0.7404 (mmtt) cc_final: 0.7119 (mmtm) REVERT: J 33 ASN cc_start: 0.8037 (m-40) cc_final: 0.7798 (t0) REVERT: J 49 MET cc_start: 0.7297 (mmt) cc_final: 0.6942 (mmt) REVERT: J 72 MET cc_start: 0.4957 (mmp) cc_final: 0.4452 (mmp) outliers start: 178 outliers final: 129 residues processed: 625 average time/residue: 0.3788 time to fit residues: 400.5811 Evaluate side-chains 634 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 490 time to evaluate : 3.319 ------------------------------------------------------------------------------- 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 306 PHE 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 754 LEU 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 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 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 105 THR 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 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 740 MET Chi-restraints excluded: chain E residue 742 ILE 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 907 ASN Chi-restraints excluded: chain E residue 916 LEU 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 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 223 LEU 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 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 552 LEU Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 907 ASN 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 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 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 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 300 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 213 optimal weight: 0.3980 chunk 192 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 0.0270 chunk 120 optimal weight: 9.9990 chunk 357 optimal weight: 0.9980 chunk 151 optimal weight: 0.0020 overall best weight: 0.4846 ------------------------------------------------------------------------------- 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 ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 895 GLN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 762 GLN F1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.219481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.128064 restraints weight = 39689.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.133491 restraints weight = 21292.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.135864 restraints weight = 14322.079| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1911 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= 0.123 Angle : 0.576 11.880 45224 Z= 0.287 Chirality : 0.045 0.413 5232 Planarity : 0.004 0.058 5767 Dihedral : 5.592 54.535 5150 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.49 % Allowed : 20.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4062 helix: 1.71 (0.20), residues: 681 sheet: 0.03 (0.16), residues: 1047 loop : -0.81 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 189 HIS 0.003 0.001 HIS E 655 PHE 0.015 0.001 PHE E 898 TYR 0.023 0.001 TYR D 51 ARG 0.012 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 32) link_NAG-ASN : angle 2.78954 ( 96) link_BETA1-4 : bond 0.00396 ( 4) link_BETA1-4 : angle 2.04271 ( 12) hydrogen bonds : bond 0.03434 ( 1249) hydrogen bonds : angle 5.35269 ( 3492) SS BOND : bond 0.00290 ( 23) SS BOND : angle 1.39035 ( 46) covalent geometry : bond 0.00289 (33087) covalent geometry : angle 0.55925 (45070) *********************** 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 673 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 512 time to evaluate : 3.450 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 92 PHE cc_start: 0.8323 (t80) cc_final: 0.8082 (t80) REVERT: A 191 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: A 289 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8162 (p) REVERT: A 347 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6472 (t80) REVERT: A 378 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7494 (ttmm) REVERT: A 794 ILE cc_start: 0.7981 (mt) cc_final: 0.7494 (tt) REVERT: A 796 ASP cc_start: 0.7967 (t0) cc_final: 0.7524 (m-30) REVERT: A 821 LEU cc_start: 0.8651 (tp) cc_final: 0.8378 (tt) REVERT: A 935 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: A 979 ASP cc_start: 0.7462 (t0) cc_final: 0.7199 (t0) REVERT: A 1101 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.6951 (p-80) REVERT: C 215 LYS cc_start: 0.8368 (tppt) cc_final: 0.7633 (mtmt) REVERT: D 49 MET cc_start: 0.7265 (mmt) cc_final: 0.7018 (mmt) REVERT: D 208 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8035 (tptp) REVERT: E 33 THR cc_start: 0.9160 (p) cc_final: 0.8769 (t) REVERT: E 58 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: E 221 SER cc_start: 0.9014 (t) cc_final: 0.8799 (m) REVERT: E 280 ASN cc_start: 0.7928 (t0) cc_final: 0.7676 (t0) REVERT: E 318 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7618 (p90) REVERT: E 531 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8547 (p) REVERT: E 619 GLU cc_start: 0.7986 (mp0) cc_final: 0.7785 (mp0) REVERT: E 740 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7868 (ttt) REVERT: E 787 GLN cc_start: 0.8306 (pt0) cc_final: 0.8004 (pt0) REVERT: E 916 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8164 (tp) REVERT: F 53 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: F 221 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7768 (m) REVERT: F 239 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: F 274 THR cc_start: 0.7261 (m) cc_final: 0.6892 (p) REVERT: F 314 GLN cc_start: 0.8508 (tt0) cc_final: 0.8154 (tp40) REVERT: F 319 ARG cc_start: 0.7485 (ptp-110) cc_final: 0.6884 (ptp-110) REVERT: F 357 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7917 (ttp80) REVERT: F 390 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8573 (mm) REVERT: F 493 GLN cc_start: 0.8035 (tp40) cc_final: 0.7739 (tm-30) REVERT: F 529 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8509 (mtmm) REVERT: F 558 LYS cc_start: 0.8869 (pttp) cc_final: 0.8560 (pttm) REVERT: F 588 THR cc_start: 0.8820 (m) cc_final: 0.8501 (p) REVERT: F 823 PHE cc_start: 0.7619 (t80) cc_final: 0.7341 (m-80) REVERT: F 909 ILE cc_start: 0.9061 (pt) cc_final: 0.8850 (pt) REVERT: F 957 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: F 978 ASN cc_start: 0.8485 (t0) cc_final: 0.8173 (t0) REVERT: F 1084 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: H 40 ARG cc_start: 0.7365 (ptt180) cc_final: 0.7092 (ptt90) REVERT: J 49 MET cc_start: 0.7231 (mmt) cc_final: 0.6714 (mmt) REVERT: J 72 MET cc_start: 0.4914 (mmp) cc_final: 0.4404 (mmp) outliers start: 161 outliers final: 125 residues processed: 626 average time/residue: 0.3705 time to fit residues: 395.0312 Evaluate side-chains 640 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 499 time to evaluate : 3.259 ------------------------------------------------------------------------------- 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 306 PHE 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 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 94 THR 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 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 105 THR Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 107 LEU 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 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 595 VAL 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 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 727 LEU 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 742 ILE 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 916 LEU 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 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 144 TYR 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 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 599 THR Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 907 ASN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 212 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 804 GLN A 935 GLN A 955 ASN A1005 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 907 ASN E 935 GLN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.218591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.128117 restraints weight = 39679.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.132104 restraints weight = 22322.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.133473 restraints weight = 15570.125| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33146 Z= 0.182 Angle : 0.600 11.682 45224 Z= 0.300 Chirality : 0.046 0.342 5232 Planarity : 0.004 0.058 5767 Dihedral : 5.639 54.637 5150 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.80 % Allowed : 20.31 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4062 helix: 1.56 (0.20), residues: 686 sheet: 0.00 (0.16), residues: 1068 loop : -0.82 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 189 HIS 0.006 0.001 HIS A1083 PHE 0.028 0.001 PHE A 168 TYR 0.027 0.001 TYR D 51 ARG 0.016 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 32) link_NAG-ASN : angle 2.78566 ( 96) link_BETA1-4 : bond 0.00283 ( 4) link_BETA1-4 : angle 2.02798 ( 12) hydrogen bonds : bond 0.03661 ( 1249) hydrogen bonds : angle 5.39998 ( 3492) SS BOND : bond 0.00304 ( 23) SS BOND : angle 1.53694 ( 46) covalent geometry : bond 0.00436 (33087) covalent geometry : angle 0.58462 (45070) *********************** 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 676 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 504 time to evaluate : 3.289 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 92 PHE cc_start: 0.8338 (t80) cc_final: 0.8112 (t80) REVERT: A 191 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: A 289 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 314 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: A 347 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6327 (t80) REVERT: A 794 ILE cc_start: 0.7989 (mt) cc_final: 0.7467 (tt) REVERT: A 796 ASP cc_start: 0.8015 (t0) cc_final: 0.7526 (m-30) REVERT: A 931 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 935 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: A 979 ASP cc_start: 0.7520 (t0) cc_final: 0.7204 (t0) REVERT: A 1101 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7079 (p-80) REVERT: C 215 LYS cc_start: 0.8393 (tppt) cc_final: 0.7692 (mtmt) REVERT: D 49 MET cc_start: 0.7333 (mmt) cc_final: 0.7066 (mmt) REVERT: D 208 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7956 (tptp) REVERT: E 33 THR cc_start: 0.9141 (p) cc_final: 0.8725 (t) REVERT: E 58 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: E 318 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7937 (p90) REVERT: E 531 THR cc_start: 0.8888 (m) cc_final: 0.8506 (p) REVERT: E 787 GLN cc_start: 0.8336 (pt0) cc_final: 0.8018 (pt0) REVERT: E 916 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (tp) REVERT: E 1126 CYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7830 (p) REVERT: F 33 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8232 (p) REVERT: F 53 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: F 221 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7801 (m) REVERT: F 239 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: F 274 THR cc_start: 0.7272 (m) cc_final: 0.6906 (p) REVERT: F 357 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7960 (ttp80) REVERT: F 390 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8643 (mm) REVERT: F 493 GLN cc_start: 0.7977 (tp40) cc_final: 0.7720 (tm-30) REVERT: F 529 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8435 (mtmm) REVERT: F 558 LYS cc_start: 0.8887 (pttp) cc_final: 0.8576 (pttm) REVERT: F 651 ILE cc_start: 0.9234 (tp) cc_final: 0.8848 (mt) REVERT: F 823 PHE cc_start: 0.7685 (t80) cc_final: 0.7383 (m-80) REVERT: F 978 ASN cc_start: 0.8499 (t0) cc_final: 0.8177 (t0) REVERT: F 1084 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: H 38 TRP cc_start: 0.7529 (m100) cc_final: 0.6808 (m100) REVERT: H 40 ARG cc_start: 0.7403 (ptt180) cc_final: 0.7087 (ptt90) REVERT: H 135 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7195 (mmtm) REVERT: H 165 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6133 (pp) REVERT: J 33 ASN cc_start: 0.8071 (m-40) cc_final: 0.7834 (t0) REVERT: J 49 MET cc_start: 0.7289 (mmt) cc_final: 0.6762 (mmt) REVERT: J 72 MET cc_start: 0.4899 (mmp) cc_final: 0.4381 (mmp) outliers start: 172 outliers final: 133 residues processed: 620 average time/residue: 0.3651 time to fit residues: 385.2629 Evaluate side-chains 645 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 494 time to evaluate : 3.237 ------------------------------------------------------------------------------- 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 306 PHE 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 754 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN 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 A residue 1101 HIS Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 6 GLU 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 10 VAL 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 105 THR Chi-restraints excluded: chain D residue 107 LEU 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 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 734 THR Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 742 ILE 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 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 963 VAL 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 1126 CYS 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 144 TYR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 223 LEU 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 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 494 SER 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 552 LEU 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 723 THR Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 805 ILE 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 1116 THR 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 81 VAL Chi-restraints excluded: chain H residue 165 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 247 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 324 optimal weight: 0.3980 chunk 187 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 804 GLN A 955 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN E 935 GLN F1010 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.225171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.133930 restraints weight = 39793.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.138467 restraints weight = 23628.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.140166 restraints weight = 14848.472| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33146 Z= 0.180 Angle : 0.608 11.812 45224 Z= 0.305 Chirality : 0.046 0.335 5232 Planarity : 0.004 0.061 5767 Dihedral : 5.631 54.569 5149 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.77 % Allowed : 20.51 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4062 helix: 1.56 (0.20), residues: 686 sheet: 0.01 (0.16), residues: 1068 loop : -0.83 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 189 HIS 0.004 0.001 HIS C 100 PHE 0.025 0.001 PHE A 168 TYR 0.026 0.001 TYR D 51 ARG 0.009 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 32) link_NAG-ASN : angle 2.75458 ( 96) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 2.03952 ( 12) hydrogen bonds : bond 0.03659 ( 1249) hydrogen bonds : angle 5.39658 ( 3492) SS BOND : bond 0.00325 ( 23) SS BOND : angle 1.52096 ( 46) covalent geometry : bond 0.00431 (33087) covalent geometry : angle 0.59303 (45070) *********************** 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 671 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 500 time to evaluate : 4.440 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 92 PHE cc_start: 0.8370 (t80) cc_final: 0.8139 (t80) REVERT: A 191 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: A 289 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 314 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 347 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6317 (t80) REVERT: A 794 ILE cc_start: 0.7993 (mt) cc_final: 0.7486 (tt) REVERT: A 796 ASP cc_start: 0.7990 (t0) cc_final: 0.7533 (m-30) REVERT: A 804 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8339 (mm-40) REVERT: A 821 LEU cc_start: 0.8650 (tp) cc_final: 0.8406 (tt) REVERT: A 918 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 931 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8644 (tt) REVERT: A 935 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: A 979 ASP cc_start: 0.7489 (t0) cc_final: 0.7192 (t0) REVERT: A 985 ASP cc_start: 0.8239 (t0) cc_final: 0.7949 (t0) REVERT: A 1101 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7082 (p-80) REVERT: C 215 LYS cc_start: 0.8368 (tppt) cc_final: 0.7567 (mtmt) REVERT: D 49 MET cc_start: 0.7351 (mmt) cc_final: 0.7110 (mmt) REVERT: D 208 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7973 (tptp) REVERT: E 33 THR cc_start: 0.9100 (p) cc_final: 0.8594 (t) REVERT: E 58 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: E 318 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7910 (p90) REVERT: E 531 THR cc_start: 0.8952 (m) cc_final: 0.8550 (p) REVERT: E 916 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8199 (tp) REVERT: F 33 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8255 (p) REVERT: F 53 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: F 221 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7858 (m) REVERT: F 239 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: F 274 THR cc_start: 0.7261 (m) cc_final: 0.6877 (p) REVERT: F 357 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7933 (ttp80) REVERT: F 390 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8637 (mm) REVERT: F 493 GLN cc_start: 0.7994 (tp40) cc_final: 0.7758 (tm-30) REVERT: F 529 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8443 (mtmm) REVERT: F 532 ASN cc_start: 0.8374 (m-40) cc_final: 0.8010 (p0) REVERT: F 558 LYS cc_start: 0.8884 (pttp) cc_final: 0.8568 (pttm) REVERT: F 651 ILE cc_start: 0.9246 (tp) cc_final: 0.8921 (mt) REVERT: F 823 PHE cc_start: 0.7695 (t80) cc_final: 0.7416 (m-80) REVERT: F 957 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: F 978 ASN cc_start: 0.8473 (t0) cc_final: 0.8167 (t0) REVERT: F 1084 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: H 38 TRP cc_start: 0.7455 (m100) cc_final: 0.6689 (m100) REVERT: H 40 ARG cc_start: 0.7385 (ptt180) cc_final: 0.7118 (ptt90) REVERT: H 68 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7879 (mtp-110) REVERT: H 135 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7211 (mmtt) REVERT: H 165 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6121 (pp) REVERT: J 33 ASN cc_start: 0.8062 (m-40) cc_final: 0.7821 (t0) REVERT: J 49 MET cc_start: 0.7227 (mmt) cc_final: 0.6751 (mmt) REVERT: J 72 MET cc_start: 0.4891 (mmp) cc_final: 0.4357 (mmp) outliers start: 171 outliers final: 134 residues processed: 615 average time/residue: 0.3845 time to fit residues: 404.3506 Evaluate side-chains 643 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 489 time to evaluate : 3.320 ------------------------------------------------------------------------------- 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 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 306 PHE 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 382 VAL 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 754 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN 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 A residue 1101 HIS Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 10 VAL 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 105 THR 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 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 608 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 734 THR Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 742 ILE 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 820 ASP Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 963 VAL 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 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 144 TYR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 223 LEU 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 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 534 VAL Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 907 ASN 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 1116 THR 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 81 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 284 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 chunk 302 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 314 optimal weight: 0.2980 chunk 237 optimal weight: 0.3980 chunk 399 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 324 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 804 GLN A 935 GLN A 955 ASN A1036 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN E 907 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.229839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.138208 restraints weight = 39889.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.144094 restraints weight = 20687.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.147172 restraints weight = 13551.695| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33146 Z= 0.130 Angle : 0.592 11.891 45224 Z= 0.296 Chirality : 0.045 0.322 5232 Planarity : 0.004 0.063 5767 Dihedral : 5.546 54.608 5149 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.58 % Allowed : 20.70 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4062 helix: 1.67 (0.20), residues: 686 sheet: 0.05 (0.16), residues: 1070 loop : -0.79 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 189 HIS 0.004 0.001 HIS A1083 PHE 0.029 0.001 PHE A 429 TYR 0.022 0.001 TYR D 51 ARG 0.008 0.000 ARG F 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00873 ( 32) link_NAG-ASN : angle 2.68312 ( 96) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 2.01771 ( 12) hydrogen bonds : bond 0.03478 ( 1249) hydrogen bonds : angle 5.32163 ( 3492) SS BOND : bond 0.00280 ( 23) SS BOND : angle 1.37381 ( 46) covalent geometry : bond 0.00308 (33087) covalent geometry : angle 0.57760 (45070) ********************** 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 664 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 500 time to evaluate : 3.236 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 92 PHE cc_start: 0.8296 (t80) cc_final: 0.8068 (t80) REVERT: A 191 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 289 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 347 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6308 (t80) REVERT: A 794 ILE cc_start: 0.7983 (mt) cc_final: 0.7489 (tt) REVERT: A 796 ASP cc_start: 0.7951 (t0) cc_final: 0.7521 (m-30) REVERT: A 918 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: A 931 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8581 (tt) REVERT: A 979 ASP cc_start: 0.7513 (t0) cc_final: 0.7245 (t0) REVERT: A 985 ASP cc_start: 0.8232 (t0) cc_final: 0.7948 (t0) REVERT: A 1005 GLN cc_start: 0.8010 (tt0) cc_final: 0.7739 (tt0) REVERT: A 1101 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6921 (p-80) REVERT: A 1102 TRP cc_start: 0.8928 (m100) cc_final: 0.8452 (m100) REVERT: C 215 LYS cc_start: 0.8353 (tppt) cc_final: 0.7643 (mtmt) REVERT: D 49 MET cc_start: 0.7298 (mmt) cc_final: 0.7067 (mmt) REVERT: D 208 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7966 (tptp) REVERT: E 58 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: E 318 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7728 (p90) REVERT: E 531 THR cc_start: 0.8910 (m) cc_final: 0.8506 (p) REVERT: E 619 GLU cc_start: 0.8253 (mp0) cc_final: 0.8037 (mp0) REVERT: E 787 GLN cc_start: 0.8296 (pt0) cc_final: 0.7981 (pt0) REVERT: E 916 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8159 (tp) REVERT: F 33 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8230 (p) REVERT: F 53 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: F 221 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7772 (m) REVERT: F 239 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: F 274 THR cc_start: 0.7169 (m) cc_final: 0.6773 (p) REVERT: F 314 GLN cc_start: 0.8535 (tt0) cc_final: 0.8164 (tp40) REVERT: F 357 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7943 (ttp80) REVERT: F 390 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8590 (mm) REVERT: F 493 GLN cc_start: 0.7996 (tp40) cc_final: 0.7732 (tm-30) REVERT: F 529 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8430 (mtmm) REVERT: F 532 ASN cc_start: 0.8350 (m-40) cc_final: 0.7929 (p0) REVERT: F 558 LYS cc_start: 0.8863 (pttp) cc_final: 0.8562 (pttm) REVERT: F 823 PHE cc_start: 0.7649 (t80) cc_final: 0.7370 (m-80) REVERT: F 935 GLN cc_start: 0.7567 (tt0) cc_final: 0.7170 (tt0) REVERT: F 957 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: F 978 ASN cc_start: 0.8459 (t0) cc_final: 0.8165 (t0) REVERT: F 1084 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: H 38 TRP cc_start: 0.7483 (m100) cc_final: 0.6675 (m100) REVERT: H 68 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7918 (mtp-110) REVERT: H 74 ASP cc_start: 0.7417 (t70) cc_final: 0.7062 (t70) REVERT: H 135 LYS cc_start: 0.7413 (mmtt) cc_final: 0.7194 (mmtt) REVERT: H 165 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6091 (pp) REVERT: J 33 ASN cc_start: 0.8052 (m-40) cc_final: 0.7813 (t0) REVERT: J 49 MET cc_start: 0.7258 (mmt) cc_final: 0.6730 (mmt) REVERT: J 72 MET cc_start: 0.4862 (mmp) cc_final: 0.4333 (mmp) outliers start: 164 outliers final: 135 residues processed: 614 average time/residue: 0.3640 time to fit residues: 378.7948 Evaluate side-chains 644 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 492 time to evaluate : 3.454 ------------------------------------------------------------------------------- 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 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 306 PHE 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 382 VAL 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 1082 CYS 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 6 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 10 VAL 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 105 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 112 GLN 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 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 615 VAL 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 743 CYS 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 916 LEU Chi-restraints excluded: chain E residue 963 VAL 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 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 33 THR Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 144 TYR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 223 LEU 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 494 SER 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 534 VAL Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 649 CYS Chi-restraints excluded: chain F residue 743 CYS Chi-restraints excluded: chain F residue 805 ILE Chi-restraints excluded: chain F residue 884 SER Chi-restraints excluded: chain F residue 894 LEU Chi-restraints excluded: chain F residue 907 ASN Chi-restraints excluded: chain F residue 957 GLN 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 379 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 358 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 316 optimal weight: 0.0050 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 A1036 GLN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.229736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.140087 restraints weight = 39962.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.145061 restraints weight = 21866.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.146359 restraints weight = 14536.887| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2169 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= 0.137 Angle : 0.591 11.953 45224 Z= 0.294 Chirality : 0.045 0.313 5232 Planarity : 0.004 0.065 5767 Dihedral : 5.511 54.722 5148 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.19 % Allowed : 21.23 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4062 helix: 1.66 (0.20), residues: 688 sheet: 0.05 (0.16), residues: 1074 loop : -0.79 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 189 HIS 0.004 0.001 HIS J 40 PHE 0.028 0.001 PHE A 168 TYR 0.023 0.001 TYR D 51 ARG 0.008 0.000 ARG H 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 32) link_NAG-ASN : angle 2.65338 ( 96) link_BETA1-4 : bond 0.00341 ( 4) link_BETA1-4 : angle 1.98785 ( 12) hydrogen bonds : bond 0.03459 ( 1249) hydrogen bonds : angle 5.27877 ( 3492) SS BOND : bond 0.00286 ( 23) SS BOND : angle 1.37180 ( 46) covalent geometry : bond 0.00326 (33087) covalent geometry : angle 0.57617 (45070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12691.86 seconds wall clock time: 222 minutes 53.67 seconds (13373.67 seconds total)