Starting phenix.real_space_refine on Thu Jun 26 19:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz9_26883/06_2025/7uz9_26883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz9_26883/06_2025/7uz9_26883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz9_26883/06_2025/7uz9_26883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz9_26883/06_2025/7uz9_26883.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz9_26883/06_2025/7uz9_26883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz9_26883/06_2025/7uz9_26883.cif" } resolution = 3.5 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= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19515 2.51 5 N 5040 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30669 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "M" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "P" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 16.55, per 1000 atoms: 0.54 Number of scatterers: 30669 At special positions: 0 Unit cell: (158.08, 178.88, 196.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5982 8.00 N 5040 7.00 C 19515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 122 " " NAG A1314 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 122 " " NAG B1314 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 122 " " NAG C1314 " - " ASN C 282 " Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 3.7 seconds 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 65 sheets defined 22.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.505A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.091A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.599A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.751A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.898A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.952A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.997A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.603A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.165A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.982A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.650A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1147' Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.634A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.703A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.616A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.640A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.574A pdb=" N SER C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.730A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.732A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.216A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.529A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1147' Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.560A pdb=" N SER H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.813A pdb=" N VAL L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'N' and resid 95 through 99 removed outlier: 3.707A pdb=" N VAL N 99 " --> pdb=" O ALA N 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.648A pdb=" N TYR P 37 " --> pdb=" O PHE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.790A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.134A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.951A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.161A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146 removed outlier: 7.428A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.461A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.004A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.929A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.792A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.936A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 723 removed outlier: 3.555A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 723 removed outlier: 3.555A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.510A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.563A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.921A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.882A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 145 removed outlier: 6.864A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.451A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.985A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.664A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.595A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.824A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 723 removed outlier: 3.789A pdb=" N VAL B1060 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 723 Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.545A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.431A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.773A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 70 removed outlier: 3.542A pdb=" N HIS C 69 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.575A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 142 through 146 removed outlier: 7.220A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.417A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.843A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.798A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.856A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.801A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.802A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.526A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.559A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 13 removed outlier: 6.459A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.620A pdb=" N ILE L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 55 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.698A pdb=" N THR L 117 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.626A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP M 38 " --> pdb=" O TYR M 107 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE M 39 " --> pdb=" O ASP M 55 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP M 55 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG M 64 " --> pdb=" O TYR M 57 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.626A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG M 106 " --> pdb=" O TYR M 117 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR M 117 " --> pdb=" O ARG M 106 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.746A pdb=" N ILE N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR N 55 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AG6, first strand: chain 'P' and resid 3 through 5 removed outlier: 3.513A pdb=" N SER P 26 " --> pdb=" O GLN P 3 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN P 5 " --> pdb=" O LYS P 24 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS P 24 " --> pdb=" O GLN P 5 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.545A pdb=" N GLU P 11 " --> pdb=" O THR P 125 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY P 54 " --> pdb=" O TRP P 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG P 64 " --> pdb=" O TYR P 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Q 39 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR Q 55 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR Q 117 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 30 through 31 1174 hydrogen bonds defined for protein. 3111 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: 13.70 Time building geometry restraints manager: 8.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9800 1.35 - 1.47: 7960 1.47 - 1.59: 13458 1.59 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 31389 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 ... (remaining 31384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 42101 2.10 - 4.19: 593 4.19 - 6.29: 39 6.29 - 8.38: 9 8.38 - 10.48: 5 Bond angle restraints: 42747 Sorted by residual: angle pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " pdb=" NE ARG B 273 " ideal model delta sigma weight residual 112.00 101.83 10.17 2.20e+00 2.07e-01 2.14e+01 angle pdb=" N VAL M 111A" pdb=" CA VAL M 111A" pdb=" C VAL M 111A" ideal model delta sigma weight residual 112.98 109.16 3.82 1.25e+00 6.40e-01 9.36e+00 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.71 110.93 2.78 9.50e-01 1.11e+00 8.58e+00 angle pdb=" C TYR H 112 " pdb=" CA TYR H 112 " pdb=" CB TYR H 112 " ideal model delta sigma weight residual 110.42 116.03 -5.61 1.99e+00 2.53e-01 7.94e+00 ... (remaining 42742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 18026 23.09 - 46.18: 912 46.18 - 69.27: 95 69.27 - 92.37: 43 92.37 - 115.46: 76 Dihedral angle restraints: 19152 sinusoidal: 7896 harmonic: 11256 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 7.45 85.55 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 104 " pdb=" CB CYS P 104 " ideal model delta sinusoidal sigma weight residual 93.00 36.09 56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA TRP A 886 " pdb=" C TRP A 886 " pdb=" N THR A 887 " pdb=" CA THR A 887 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 19149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4703 0.099 - 0.198: 206 0.198 - 0.297: 9 0.297 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4917 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 273 " 0.398 9.50e-02 1.11e+02 1.78e-01 2.01e+01 pdb=" NE ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 273 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 273 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 579 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO C 85 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1267 2.72 - 3.27: 30860 3.27 - 3.81: 49793 3.81 - 4.36: 58865 4.36 - 4.90: 99897 Nonbonded interactions: 240682 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.175 3.040 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.188 3.040 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.188 3.120 nonbonded pdb=" O MET C 731 " pdb=" NE2 GLN C 774 " model vdw 2.197 3.120 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.200 3.040 ... (remaining 240677 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.020 Extract box with map and model: 1.420 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 68.200 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31473 Z= 0.165 Angle : 0.608 10.480 42957 Z= 0.310 Chirality : 0.045 0.494 4920 Planarity : 0.005 0.178 5481 Dihedral : 15.469 115.458 11820 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.31 (0.13), residues: 3825 helix: 1.26 (0.20), residues: 680 sheet: 0.57 (0.17), residues: 910 loop : -0.23 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 886 HIS 0.005 0.001 HIS B 49 PHE 0.022 0.002 PHE C 86 TYR 0.020 0.001 TYR B 904 ARG 0.014 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 2.68737 ( 126) hydrogen bonds : bond 0.23873 ( 1154) hydrogen bonds : angle 8.83553 ( 3111) SS BOND : bond 0.00209 ( 42) SS BOND : angle 0.95912 ( 84) covalent geometry : bond 0.00344 (31389) covalent geometry : angle 0.58974 (42747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 894 LEU cc_start: 0.8079 (mt) cc_final: 0.7863 (mm) REVERT: B 53 ASP cc_start: 0.8113 (t0) cc_final: 0.7722 (t70) REVERT: B 54 LEU cc_start: 0.8678 (mm) cc_final: 0.8441 (mm) REVERT: B 55 PHE cc_start: 0.7374 (m-80) cc_final: 0.7095 (m-80) REVERT: B 128 ILE cc_start: 0.8956 (mm) cc_final: 0.8608 (mm) REVERT: B 170 TYR cc_start: 0.8768 (t80) cc_final: 0.8303 (t80) REVERT: B 707 TYR cc_start: 0.8054 (t80) cc_final: 0.7273 (t80) REVERT: B 1082 CYS cc_start: 0.6596 (t) cc_final: 0.6276 (t) REVERT: B 1139 ASP cc_start: 0.8241 (m-30) cc_final: 0.8032 (t0) REVERT: C 196 ASN cc_start: 0.7825 (t0) cc_final: 0.7548 (t0) REVERT: C 584 ILE cc_start: 0.7840 (mm) cc_final: 0.7429 (mm) REVERT: C 658 ASN cc_start: 0.8117 (t0) cc_final: 0.7438 (t0) REVERT: C 675 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8041 (tm-30) REVERT: C 699 LEU cc_start: 0.7858 (tp) cc_final: 0.7438 (mt) REVERT: C 755 GLN cc_start: 0.7692 (pp30) cc_final: 0.7484 (pp30) REVERT: M 38 TRP cc_start: 0.7381 (m-90) cc_final: 0.6855 (m-90) REVERT: M 110 ASN cc_start: 0.8069 (t0) cc_final: 0.7593 (t0) REVERT: P 21 MET cc_start: 0.2346 (tpt) cc_final: -0.0786 (pmm) REVERT: P 115 MET cc_start: 0.3253 (tpt) cc_final: 0.2725 (tpp) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.3584 time to fit residues: 233.7601 Evaluate side-chains 301 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 348 optimal weight: 40.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 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 = 0.4589 r_free = 0.4589 target = 0.204540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114609 restraints weight = 51373.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119327 restraints weight = 23079.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120552 restraints weight = 12131.795| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31473 Z= 0.210 Angle : 0.690 17.871 42957 Z= 0.342 Chirality : 0.049 0.394 4920 Planarity : 0.005 0.126 5481 Dihedral : 11.598 113.347 5064 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.91 % Allowed : 8.53 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3825 helix: 1.03 (0.19), residues: 695 sheet: 0.66 (0.17), residues: 948 loop : -0.22 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.011 0.001 HIS B 49 PHE 0.025 0.002 PHE C 562 TYR 0.017 0.001 TYR A 204 ARG 0.009 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 42) link_NAG-ASN : angle 3.10199 ( 126) hydrogen bonds : bond 0.05073 ( 1154) hydrogen bonds : angle 6.86720 ( 3111) SS BOND : bond 0.00303 ( 42) SS BOND : angle 1.08293 ( 84) covalent geometry : bond 0.00472 (31389) covalent geometry : angle 0.66932 (42747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 328 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.6492 (t80) cc_final: 0.6166 (t80) REVERT: A 610 VAL cc_start: 0.8968 (t) cc_final: 0.8636 (p) REVERT: B 53 ASP cc_start: 0.8122 (t0) cc_final: 0.7626 (t70) REVERT: B 54 LEU cc_start: 0.8800 (mm) cc_final: 0.8536 (mm) REVERT: B 55 PHE cc_start: 0.7339 (m-80) cc_final: 0.7064 (m-80) REVERT: B 707 TYR cc_start: 0.8412 (t80) cc_final: 0.7503 (t80) REVERT: B 741 TYR cc_start: 0.7967 (t80) cc_final: 0.7706 (t80) REVERT: B 968 SER cc_start: 0.9034 (p) cc_final: 0.8812 (p) REVERT: B 970 PHE cc_start: 0.7675 (m-80) cc_final: 0.7022 (m-80) REVERT: B 1082 CYS cc_start: 0.6546 (t) cc_final: 0.6193 (t) REVERT: B 1139 ASP cc_start: 0.8145 (m-30) cc_final: 0.7883 (t0) REVERT: C 592 PHE cc_start: 0.8720 (p90) cc_final: 0.8477 (p90) REVERT: C 661 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 675 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 900 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.7019 (mtm) REVERT: C 1033 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8147 (p) REVERT: L 37 SER cc_start: 0.4031 (m) cc_final: 0.3784 (t) REVERT: P 21 MET cc_start: 0.2241 (tpt) cc_final: 0.1765 (tpt) outliers start: 30 outliers final: 25 residues processed: 345 average time/residue: 0.3661 time to fit residues: 218.6023 Evaluate side-chains 323 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1033 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 143 optimal weight: 50.0000 chunk 52 optimal weight: 1.9990 chunk 357 optimal weight: 20.0000 chunk 303 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 278 optimal weight: 0.7980 chunk 284 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1048 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 = 0.4612 r_free = 0.4612 target = 0.207527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116730 restraints weight = 51102.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120956 restraints weight = 21427.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123730 restraints weight = 12551.865| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31473 Z= 0.123 Angle : 0.599 16.419 42957 Z= 0.291 Chirality : 0.046 0.340 4920 Planarity : 0.004 0.090 5481 Dihedral : 8.812 118.620 5064 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.33 % Allowed : 10.65 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.39 (0.13), residues: 3825 helix: 1.27 (0.19), residues: 694 sheet: 0.62 (0.17), residues: 982 loop : -0.19 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.013 0.001 HIS B 49 PHE 0.024 0.002 PHE C 55 TYR 0.016 0.001 TYR B 369 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 42) link_NAG-ASN : angle 2.63718 ( 126) hydrogen bonds : bond 0.04157 ( 1154) hydrogen bonds : angle 6.16141 ( 3111) SS BOND : bond 0.00278 ( 42) SS BOND : angle 1.01002 ( 84) covalent geometry : bond 0.00275 (31389) covalent geometry : angle 0.58146 (42747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 338 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7718 (m90) REVERT: A 610 VAL cc_start: 0.8985 (t) cc_final: 0.8681 (p) REVERT: A 756 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7629 (t80) REVERT: A 873 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: B 53 ASP cc_start: 0.8340 (t0) cc_final: 0.7732 (t70) REVERT: B 54 LEU cc_start: 0.8847 (mm) cc_final: 0.8411 (mm) REVERT: B 55 PHE cc_start: 0.7258 (m-80) cc_final: 0.7002 (m-80) REVERT: B 168 PHE cc_start: 0.7922 (t80) cc_final: 0.7611 (t80) REVERT: B 214 ARG cc_start: 0.8461 (mpp-170) cc_final: 0.7124 (ttt-90) REVERT: B 265 TYR cc_start: 0.5803 (p90) cc_final: 0.5544 (p90) REVERT: B 707 TYR cc_start: 0.8239 (t80) cc_final: 0.7420 (t80) REVERT: B 730 SER cc_start: 0.8557 (t) cc_final: 0.8201 (p) REVERT: B 741 TYR cc_start: 0.8058 (t80) cc_final: 0.7743 (t80) REVERT: B 901 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: B 906 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: B 1082 CYS cc_start: 0.6314 (t) cc_final: 0.6012 (t) REVERT: B 1139 ASP cc_start: 0.8181 (m-30) cc_final: 0.7933 (t0) REVERT: C 177 MET cc_start: 0.6704 (mtt) cc_final: 0.6441 (mtp) REVERT: C 196 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.7060 (t0) REVERT: C 584 ILE cc_start: 0.8089 (mm) cc_final: 0.7557 (mm) REVERT: C 592 PHE cc_start: 0.8734 (p90) cc_final: 0.8391 (p90) REVERT: C 658 ASN cc_start: 0.8192 (t0) cc_final: 0.7726 (t0) REVERT: C 661 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 675 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 731 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7158 (ptp) REVERT: C 900 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6959 (mtm) REVERT: L 37 SER cc_start: 0.4147 (m) cc_final: 0.3883 (t) REVERT: P 115 MET cc_start: 0.4265 (tpp) cc_final: 0.3850 (tpp) outliers start: 44 outliers final: 20 residues processed: 363 average time/residue: 0.3695 time to fit residues: 230.9776 Evaluate side-chains 331 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 303 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 291 optimal weight: 1.9990 chunk 190 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 354 optimal weight: 40.0000 chunk 248 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 213 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 251 optimal weight: 40.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.204394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111119 restraints weight = 52118.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116017 restraints weight = 23610.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117792 restraints weight = 12523.211| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31473 Z= 0.227 Angle : 0.663 17.709 42957 Z= 0.329 Chirality : 0.047 0.363 4920 Planarity : 0.005 0.103 5481 Dihedral : 7.891 111.255 5064 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.42 % Allowed : 12.34 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.20 (0.13), residues: 3825 helix: 0.97 (0.19), residues: 692 sheet: 0.53 (0.17), residues: 980 loop : -0.28 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 886 HIS 0.011 0.001 HIS B 49 PHE 0.033 0.002 PHE C 275 TYR 0.020 0.001 TYR C 707 ARG 0.009 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 2.80815 ( 126) hydrogen bonds : bond 0.04374 ( 1154) hydrogen bonds : angle 6.16164 ( 3111) SS BOND : bond 0.00707 ( 42) SS BOND : angle 1.06898 ( 84) covalent geometry : bond 0.00522 (31389) covalent geometry : angle 0.64465 (42747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 300 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8498 (t) REVERT: A 610 VAL cc_start: 0.9137 (t) cc_final: 0.8831 (p) REVERT: A 873 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: B 168 PHE cc_start: 0.8115 (t80) cc_final: 0.7838 (t80) REVERT: B 265 TYR cc_start: 0.5529 (p90) cc_final: 0.5223 (p90) REVERT: B 707 TYR cc_start: 0.8398 (t80) cc_final: 0.7451 (t80) REVERT: B 901 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: B 906 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: B 943 SER cc_start: 0.8379 (m) cc_final: 0.8048 (p) REVERT: B 970 PHE cc_start: 0.7970 (m-80) cc_final: 0.7691 (m-80) REVERT: C 176 LEU cc_start: 0.6984 (mm) cc_final: 0.6538 (mm) REVERT: C 584 ILE cc_start: 0.8132 (mm) cc_final: 0.7589 (mm) REVERT: C 675 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 731 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7230 (ptp) REVERT: C 823 PHE cc_start: 0.8187 (t80) cc_final: 0.7802 (t80) REVERT: L 37 SER cc_start: 0.4137 (m) cc_final: 0.3873 (t) REVERT: P 115 MET cc_start: 0.4748 (tpp) cc_final: 0.4368 (tpp) outliers start: 80 outliers final: 58 residues processed: 352 average time/residue: 0.3475 time to fit residues: 211.9688 Evaluate side-chains 339 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 85 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 179 optimal weight: 0.0970 chunk 361 optimal weight: 0.4980 chunk 231 optimal weight: 30.0000 chunk 266 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 247 optimal weight: 50.0000 chunk 292 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 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 = 0.4540 r_free = 0.4540 target = 0.205292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110850 restraints weight = 51595.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114982 restraints weight = 21992.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117530 restraints weight = 13061.897| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31473 Z= 0.115 Angle : 0.583 16.599 42957 Z= 0.286 Chirality : 0.045 0.357 4920 Planarity : 0.004 0.085 5481 Dihedral : 7.199 104.190 5064 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.66 % Allowed : 14.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.34 (0.13), residues: 3825 helix: 1.18 (0.19), residues: 692 sheet: 0.60 (0.17), residues: 980 loop : -0.22 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.013 0.001 HIS B 49 PHE 0.041 0.001 PHE C 275 TYR 0.019 0.001 TYR B 369 ARG 0.006 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 42) link_NAG-ASN : angle 2.67180 ( 126) hydrogen bonds : bond 0.03775 ( 1154) hydrogen bonds : angle 5.72650 ( 3111) SS BOND : bond 0.00267 ( 42) SS BOND : angle 1.12778 ( 84) covalent geometry : bond 0.00260 (31389) covalent geometry : angle 0.56421 (42747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 305 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7779 (mp10) REVERT: A 318 PHE cc_start: 0.8529 (t80) cc_final: 0.8158 (t80) REVERT: A 610 VAL cc_start: 0.8971 (t) cc_final: 0.8674 (p) REVERT: A 699 LEU cc_start: 0.8007 (tt) cc_final: 0.7476 (tt) REVERT: A 756 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7668 (t80) REVERT: A 873 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: A 895 GLN cc_start: 0.7630 (pp30) cc_final: 0.7019 (pp30) REVERT: B 168 PHE cc_start: 0.8117 (t80) cc_final: 0.7860 (t80) REVERT: B 214 ARG cc_start: 0.8503 (mpp-170) cc_final: 0.7112 (tmt170) REVERT: B 265 TYR cc_start: 0.5524 (p90) cc_final: 0.5298 (p90) REVERT: B 707 TYR cc_start: 0.8302 (t80) cc_final: 0.7187 (t80) REVERT: B 730 SER cc_start: 0.8644 (t) cc_final: 0.8186 (p) REVERT: B 741 TYR cc_start: 0.7981 (t80) cc_final: 0.7741 (t80) REVERT: B 754 LEU cc_start: 0.8923 (tp) cc_final: 0.8549 (pp) REVERT: B 873 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B 895 GLN cc_start: 0.7346 (pp30) cc_final: 0.6993 (pp30) REVERT: B 901 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: B 906 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: B 943 SER cc_start: 0.8422 (m) cc_final: 0.8104 (p) REVERT: C 38 TYR cc_start: 0.7946 (m-80) cc_final: 0.7510 (m-80) REVERT: C 196 ASN cc_start: 0.7597 (p0) cc_final: 0.6602 (t0) REVERT: C 584 ILE cc_start: 0.8081 (mm) cc_final: 0.7533 (mm) REVERT: C 661 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 675 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 731 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7196 (ptp) REVERT: C 872 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: C 900 MET cc_start: 0.7381 (mtm) cc_final: 0.7069 (mtt) REVERT: C 1107 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7370 (ttm170) REVERT: L 37 SER cc_start: 0.3881 (m) cc_final: 0.3645 (t) REVERT: P 115 MET cc_start: 0.5326 (tpp) cc_final: 0.4894 (tpp) outliers start: 55 outliers final: 34 residues processed: 342 average time/residue: 0.3725 time to fit residues: 217.8362 Evaluate side-chains 323 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 242 optimal weight: 6.9990 chunk 289 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 136 optimal weight: 30.0000 chunk 248 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 302 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.208454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117335 restraints weight = 52010.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122271 restraints weight = 24083.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124172 restraints weight = 12840.095| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31473 Z= 0.176 Angle : 0.619 17.580 42957 Z= 0.306 Chirality : 0.046 0.381 4920 Planarity : 0.005 0.086 5481 Dihedral : 7.058 102.227 5064 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.42 % Allowed : 14.64 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 3825 helix: 1.13 (0.19), residues: 686 sheet: 0.55 (0.17), residues: 986 loop : -0.29 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.011 0.001 HIS B 49 PHE 0.038 0.002 PHE C 275 TYR 0.021 0.001 TYR C 873 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 42) link_NAG-ASN : angle 2.78463 ( 126) hydrogen bonds : bond 0.03927 ( 1154) hydrogen bonds : angle 5.73144 ( 3111) SS BOND : bond 0.00346 ( 42) SS BOND : angle 1.34170 ( 84) covalent geometry : bond 0.00406 (31389) covalent geometry : angle 0.59925 (42747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7864 (mp10) REVERT: A 306 PHE cc_start: 0.7154 (m-80) cc_final: 0.6804 (m-80) REVERT: A 610 VAL cc_start: 0.9063 (t) cc_final: 0.8755 (p) REVERT: A 699 LEU cc_start: 0.8057 (tt) cc_final: 0.7472 (tt) REVERT: A 873 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: A 895 GLN cc_start: 0.7667 (pp30) cc_final: 0.6990 (pp30) REVERT: B 168 PHE cc_start: 0.8227 (t80) cc_final: 0.7956 (t80) REVERT: B 177 MET cc_start: 0.8553 (ppp) cc_final: 0.8323 (ppp) REVERT: B 214 ARG cc_start: 0.8560 (mpp-170) cc_final: 0.7160 (tmt170) REVERT: B 265 TYR cc_start: 0.5295 (p90) cc_final: 0.5028 (p90) REVERT: B 707 TYR cc_start: 0.8454 (t80) cc_final: 0.7299 (t80) REVERT: B 730 SER cc_start: 0.8593 (t) cc_final: 0.8209 (p) REVERT: B 873 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 895 GLN cc_start: 0.7408 (pp30) cc_final: 0.7007 (pp30) REVERT: B 901 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: B 906 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: B 943 SER cc_start: 0.8481 (m) cc_final: 0.8158 (p) REVERT: C 38 TYR cc_start: 0.8080 (m-80) cc_final: 0.7736 (m-10) REVERT: C 196 ASN cc_start: 0.7592 (p0) cc_final: 0.6923 (t0) REVERT: C 584 ILE cc_start: 0.8116 (mm) cc_final: 0.7616 (mm) REVERT: C 661 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 675 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 731 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7229 (ptp) REVERT: C 823 PHE cc_start: 0.8156 (t80) cc_final: 0.7745 (t80) REVERT: C 872 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: C 1107 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: H 21 MET cc_start: 0.0487 (ptt) cc_final: 0.0271 (ptt) REVERT: L 37 SER cc_start: 0.4114 (m) cc_final: 0.3851 (t) REVERT: P 115 MET cc_start: 0.5066 (tpp) cc_final: 0.4611 (tpp) outliers start: 80 outliers final: 56 residues processed: 347 average time/residue: 0.3797 time to fit residues: 226.7552 Evaluate side-chains 339 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 42 optimal weight: 0.0970 chunk 383 optimal weight: 50.0000 chunk 211 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 262 optimal weight: 6.9990 chunk 329 optimal weight: 30.0000 chunk 351 optimal weight: 50.0000 chunk 205 optimal weight: 0.6980 chunk 248 optimal weight: 0.1980 chunk 34 optimal weight: 40.0000 chunk 204 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 755 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.205753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113478 restraints weight = 51545.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118345 restraints weight = 22857.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120522 restraints weight = 12316.288| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31473 Z= 0.106 Angle : 0.579 15.862 42957 Z= 0.281 Chirality : 0.045 0.376 4920 Planarity : 0.004 0.075 5481 Dihedral : 6.713 99.613 5064 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.06 % Allowed : 15.34 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.37 (0.14), residues: 3825 helix: 1.34 (0.19), residues: 686 sheet: 0.58 (0.17), residues: 991 loop : -0.23 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.015 0.001 HIS B 49 PHE 0.031 0.001 PHE C 275 TYR 0.019 0.001 TYR B 160 ARG 0.007 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 42) link_NAG-ASN : angle 2.68539 ( 126) hydrogen bonds : bond 0.03522 ( 1154) hydrogen bonds : angle 5.42871 ( 3111) SS BOND : bond 0.00185 ( 42) SS BOND : angle 1.39671 ( 84) covalent geometry : bond 0.00239 (31389) covalent geometry : angle 0.55823 (42747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7810 (mp10) REVERT: A 284 THR cc_start: 0.8720 (m) cc_final: 0.8515 (t) REVERT: A 306 PHE cc_start: 0.6936 (m-80) cc_final: 0.6659 (m-80) REVERT: A 318 PHE cc_start: 0.8446 (t80) cc_final: 0.8070 (t80) REVERT: A 610 VAL cc_start: 0.8977 (t) cc_final: 0.8679 (p) REVERT: A 756 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 895 GLN cc_start: 0.7722 (pp30) cc_final: 0.6999 (pp30) REVERT: B 168 PHE cc_start: 0.8127 (t80) cc_final: 0.7851 (t80) REVERT: B 177 MET cc_start: 0.8560 (ppp) cc_final: 0.8337 (ppp) REVERT: B 265 TYR cc_start: 0.5381 (p90) cc_final: 0.5120 (p90) REVERT: B 707 TYR cc_start: 0.8278 (t80) cc_final: 0.7168 (t80) REVERT: B 754 LEU cc_start: 0.8915 (tp) cc_final: 0.8537 (pp) REVERT: B 777 ASN cc_start: 0.8193 (m-40) cc_final: 0.7856 (m110) REVERT: B 873 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 895 GLN cc_start: 0.7373 (pp30) cc_final: 0.6926 (pp30) REVERT: B 901 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: B 906 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: B 943 SER cc_start: 0.8421 (m) cc_final: 0.8110 (p) REVERT: B 1082 CYS cc_start: 0.6478 (t) cc_final: 0.6076 (t) REVERT: C 38 TYR cc_start: 0.8016 (m-80) cc_final: 0.7517 (m-80) REVERT: C 196 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6564 (t0) REVERT: C 584 ILE cc_start: 0.8070 (mm) cc_final: 0.7540 (mm) REVERT: C 675 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 731 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7187 (ptp) REVERT: C 872 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: C 1107 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7098 (mtp180) REVERT: H 21 MET cc_start: 0.0584 (ptt) cc_final: 0.0338 (ptt) REVERT: L 37 SER cc_start: 0.4145 (m) cc_final: 0.3871 (t) REVERT: P 115 MET cc_start: 0.5190 (tpp) cc_final: 0.4717 (tpp) outliers start: 68 outliers final: 48 residues processed: 362 average time/residue: 0.3722 time to fit residues: 232.7475 Evaluate side-chains 341 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 331 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 330 optimal weight: 50.0000 chunk 168 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 234 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 914 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 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 = 0.4548 r_free = 0.4548 target = 0.208122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115907 restraints weight = 52519.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120876 restraints weight = 23222.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122844 restraints weight = 12204.197| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31473 Z= 0.122 Angle : 0.585 16.024 42957 Z= 0.285 Chirality : 0.045 0.383 4920 Planarity : 0.004 0.072 5481 Dihedral : 6.630 98.763 5064 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 15.94 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.37 (0.14), residues: 3825 helix: 1.33 (0.19), residues: 689 sheet: 0.60 (0.17), residues: 993 loop : -0.24 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.012 0.001 HIS B 49 PHE 0.036 0.001 PHE C 275 TYR 0.023 0.001 TYR B 873 ARG 0.006 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 42) link_NAG-ASN : angle 2.68128 ( 126) hydrogen bonds : bond 0.03553 ( 1154) hydrogen bonds : angle 5.40681 ( 3111) SS BOND : bond 0.00204 ( 42) SS BOND : angle 1.34804 ( 84) covalent geometry : bond 0.00283 (31389) covalent geometry : angle 0.56472 (42747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 289 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7853 (mp10) REVERT: A 306 PHE cc_start: 0.6866 (m-80) cc_final: 0.6628 (m-80) REVERT: A 318 PHE cc_start: 0.8413 (t80) cc_final: 0.8056 (t80) REVERT: A 610 VAL cc_start: 0.8983 (t) cc_final: 0.8691 (p) REVERT: A 756 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7733 (t80) REVERT: A 895 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6830 (pp30) REVERT: B 168 PHE cc_start: 0.8122 (t80) cc_final: 0.7872 (t80) REVERT: B 177 MET cc_start: 0.8587 (ppp) cc_final: 0.8369 (ppp) REVERT: B 214 ARG cc_start: 0.8540 (mpp-170) cc_final: 0.7117 (tmt170) REVERT: B 265 TYR cc_start: 0.5358 (p90) cc_final: 0.5074 (p90) REVERT: B 275 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7077 (m-10) REVERT: B 754 LEU cc_start: 0.8921 (tp) cc_final: 0.8542 (pp) REVERT: B 856 ASN cc_start: 0.6499 (t0) cc_final: 0.5943 (m110) REVERT: B 873 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 895 GLN cc_start: 0.7367 (pp30) cc_final: 0.6928 (pp30) REVERT: B 901 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: B 906 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: B 943 SER cc_start: 0.8423 (m) cc_final: 0.8113 (p) REVERT: B 1082 CYS cc_start: 0.6455 (t) cc_final: 0.6058 (t) REVERT: C 38 TYR cc_start: 0.8063 (m-80) cc_final: 0.7551 (m-80) REVERT: C 169 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 227 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7475 (p) REVERT: C 584 ILE cc_start: 0.8083 (mm) cc_final: 0.7562 (mm) REVERT: C 675 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 731 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7301 (ptp) REVERT: C 872 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: C 1050 MET cc_start: 0.5805 (ttm) cc_final: 0.5468 (ttp) REVERT: C 1107 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7133 (ttm170) REVERT: L 37 SER cc_start: 0.4129 (m) cc_final: 0.3860 (t) REVERT: P 115 MET cc_start: 0.5301 (tpp) cc_final: 0.4823 (tpp) outliers start: 80 outliers final: 58 residues processed: 345 average time/residue: 0.3702 time to fit residues: 218.9054 Evaluate side-chains 348 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 280 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 52 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.207111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114340 restraints weight = 51487.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119532 restraints weight = 22750.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121380 restraints weight = 12150.076| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31473 Z= 0.115 Angle : 0.588 15.717 42957 Z= 0.285 Chirality : 0.045 0.389 4920 Planarity : 0.004 0.072 5481 Dihedral : 6.516 97.812 5064 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.18 % Allowed : 16.67 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.39 (0.14), residues: 3825 helix: 1.38 (0.19), residues: 689 sheet: 0.60 (0.17), residues: 999 loop : -0.22 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.012 0.001 HIS B 49 PHE 0.069 0.002 PHE A 135 TYR 0.026 0.001 TYR B 707 ARG 0.008 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 42) link_NAG-ASN : angle 2.68117 ( 126) hydrogen bonds : bond 0.03494 ( 1154) hydrogen bonds : angle 5.34817 ( 3111) SS BOND : bond 0.00194 ( 42) SS BOND : angle 1.22546 ( 84) covalent geometry : bond 0.00269 (31389) covalent geometry : angle 0.56862 (42747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7919 (mp10) REVERT: A 284 THR cc_start: 0.8706 (m) cc_final: 0.8492 (t) REVERT: A 318 PHE cc_start: 0.8423 (t80) cc_final: 0.8050 (t80) REVERT: A 610 VAL cc_start: 0.8970 (t) cc_final: 0.8690 (p) REVERT: A 756 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 895 GLN cc_start: 0.7744 (pp30) cc_final: 0.7234 (pp30) REVERT: B 81 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8082 (t0) REVERT: B 168 PHE cc_start: 0.8083 (t80) cc_final: 0.7833 (t80) REVERT: B 177 MET cc_start: 0.8613 (ppp) cc_final: 0.8383 (ppp) REVERT: B 214 ARG cc_start: 0.8504 (mpp-170) cc_final: 0.7155 (tmt170) REVERT: B 265 TYR cc_start: 0.5363 (p90) cc_final: 0.5126 (p90) REVERT: B 275 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6948 (m-10) REVERT: B 276 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (mm) REVERT: B 754 LEU cc_start: 0.8919 (tp) cc_final: 0.8541 (pp) REVERT: B 856 ASN cc_start: 0.6499 (t0) cc_final: 0.5925 (m110) REVERT: B 873 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7207 (t80) REVERT: B 895 GLN cc_start: 0.7357 (pp30) cc_final: 0.6943 (pp30) REVERT: B 901 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7188 (tm-30) REVERT: B 906 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 943 SER cc_start: 0.8445 (m) cc_final: 0.8172 (p) REVERT: B 1082 CYS cc_start: 0.6451 (t) cc_final: 0.6045 (t) REVERT: C 34 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7785 (mtp85) REVERT: C 38 TYR cc_start: 0.8041 (m-80) cc_final: 0.7524 (m-80) REVERT: C 576 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7305 (p) REVERT: C 584 ILE cc_start: 0.8080 (mm) cc_final: 0.7560 (mm) REVERT: C 675 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 731 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7326 (ptp) REVERT: C 872 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: C 984 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7414 (tp) REVERT: C 1050 MET cc_start: 0.5729 (ttm) cc_final: 0.5385 (ttp) REVERT: C 1107 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7144 (ttm170) REVERT: L 37 SER cc_start: 0.4108 (m) cc_final: 0.3841 (t) REVERT: P 115 MET cc_start: 0.5391 (tpp) cc_final: 0.4905 (tpp) outliers start: 72 outliers final: 57 residues processed: 347 average time/residue: 0.3798 time to fit residues: 227.0709 Evaluate side-chains 355 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 286 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 379 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 319 optimal weight: 0.0000 chunk 172 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.208032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116400 restraints weight = 52249.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121224 restraints weight = 23397.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123168 restraints weight = 12385.593| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31473 Z= 0.118 Angle : 0.589 15.571 42957 Z= 0.288 Chirality : 0.045 0.390 4920 Planarity : 0.004 0.074 5481 Dihedral : 6.426 97.155 5064 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.27 % Allowed : 16.88 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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 (0.14), residues: 3825 helix: 1.40 (0.19), residues: 689 sheet: 0.63 (0.17), residues: 995 loop : -0.22 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.020 0.001 HIS A 207 PHE 0.051 0.002 PHE C 86 TYR 0.028 0.001 TYR B 707 ARG 0.008 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 42) link_NAG-ASN : angle 2.66310 ( 126) hydrogen bonds : bond 0.03447 ( 1154) hydrogen bonds : angle 5.28725 ( 3111) SS BOND : bond 0.00200 ( 42) SS BOND : angle 1.18995 ( 84) covalent geometry : bond 0.00272 (31389) covalent geometry : angle 0.56991 (42747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 290 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8184 (m-80) cc_final: 0.7590 (m-80) REVERT: A 215 ASP cc_start: 0.7344 (m-30) cc_final: 0.6724 (p0) REVERT: A 271 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7968 (mp10) REVERT: A 318 PHE cc_start: 0.8391 (t80) cc_final: 0.8017 (t80) REVERT: A 610 VAL cc_start: 0.9010 (t) cc_final: 0.8753 (p) REVERT: A 756 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.7738 (t80) REVERT: A 895 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6855 (pp30) REVERT: A 957 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 168 PHE cc_start: 0.8082 (t80) cc_final: 0.7830 (t80) REVERT: B 177 MET cc_start: 0.8647 (ppp) cc_final: 0.8394 (ppp) REVERT: B 214 ARG cc_start: 0.8513 (mpp-170) cc_final: 0.7195 (tmt170) REVERT: B 265 TYR cc_start: 0.5354 (p90) cc_final: 0.5090 (p90) REVERT: B 275 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: B 276 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7967 (mm) REVERT: B 707 TYR cc_start: 0.7782 (t80) cc_final: 0.6890 (t80) REVERT: B 754 LEU cc_start: 0.8928 (tp) cc_final: 0.8557 (pp) REVERT: B 856 ASN cc_start: 0.6636 (t0) cc_final: 0.6045 (m110) REVERT: B 873 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 895 GLN cc_start: 0.7366 (pp30) cc_final: 0.6990 (pp30) REVERT: B 901 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: B 906 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: B 943 SER cc_start: 0.8421 (m) cc_final: 0.8152 (p) REVERT: B 1082 CYS cc_start: 0.6440 (t) cc_final: 0.6045 (t) REVERT: C 34 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7837 (mtp85) REVERT: C 38 TYR cc_start: 0.8038 (m-80) cc_final: 0.7579 (m-10) REVERT: C 576 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7223 (p) REVERT: C 584 ILE cc_start: 0.8114 (mm) cc_final: 0.7609 (mm) REVERT: C 587 ILE cc_start: 0.8902 (mt) cc_final: 0.8691 (mp) REVERT: C 675 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 731 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7358 (ptp) REVERT: C 984 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7450 (tp) REVERT: C 1050 MET cc_start: 0.5765 (ttm) cc_final: 0.5419 (ttp) REVERT: C 1107 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7111 (ttm170) REVERT: L 37 SER cc_start: 0.4111 (m) cc_final: 0.3846 (t) REVERT: P 115 MET cc_start: 0.5349 (tpp) cc_final: 0.4834 (tpp) outliers start: 75 outliers final: 60 residues processed: 343 average time/residue: 0.4074 time to fit residues: 241.3578 Evaluate side-chains 348 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 277 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 49 optimal weight: 0.0070 chunk 130 optimal weight: 0.0670 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 358 optimal weight: 50.0000 chunk 355 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 371 optimal weight: 40.0000 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.204374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113067 restraints weight = 52295.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117280 restraints weight = 23048.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120091 restraints weight = 13820.036| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31473 Z= 0.164 Angle : 0.613 16.597 42957 Z= 0.301 Chirality : 0.046 0.396 4920 Planarity : 0.005 0.080 5481 Dihedral : 6.473 97.288 5064 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.24 % Allowed : 17.03 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.36 (0.14), residues: 3825 helix: 1.33 (0.19), residues: 677 sheet: 0.61 (0.17), residues: 992 loop : -0.25 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.021 0.001 HIS A 207 PHE 0.047 0.002 PHE C 86 TYR 0.023 0.001 TYR B 873 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 42) link_NAG-ASN : angle 2.72661 ( 126) hydrogen bonds : bond 0.03630 ( 1154) hydrogen bonds : angle 5.36807 ( 3111) SS BOND : bond 0.00260 ( 42) SS BOND : angle 1.23347 ( 84) covalent geometry : bond 0.00382 (31389) covalent geometry : angle 0.59406 (42747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13421.64 seconds wall clock time: 233 minutes 21.11 seconds (14001.11 seconds total)