Starting phenix.real_space_refine on Sun Jul 5 22:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz9_26883/07_2026/7uz9_26883.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} 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 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 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 chiralities: 14 Time building chain proxies: 5.90, per 1000 atoms: 0.19 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 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: 0.96 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: 7.92 Time building geometry restraints manager: 2.68 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 - 17.90: 16770 17.90 - 35.81: 1231 35.81 - 53.71: 196 53.71 - 71.61: 38 71.61 - 89.52: 35 Dihedral angle restraints: 18270 sinusoidal: 7014 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 18267 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: 0.03 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.350 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 12.951 89.517 10938 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.63 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (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 ARG 0.014 0.000 ARG B 273 TYR 0.020 0.001 TYR B 904 PHE 0.022 0.002 PHE C 86 TRP 0.041 0.001 TRP A 886 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (31389) covalent geometry : angle 0.58974 / 0.31 (42747) SS BOND : bond 0.00209 / 0.14 ( 42) SS BOND : angle 0.95912 / 0.68 ( 84) hydrogen bonds : bond 0.23873 / 15.91 ( 1154) hydrogen bonds : angle 8.83553 / 6.15 ( 3111) link_NAG-ASN : bond 0.00552 / 0.39 ( 42) link_NAG-ASN : angle 2.68737 / 1.67 ( 126) *********************** 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 : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8696 (mm) cc_final: 0.8248 (mt) REVERT: A 596 SER cc_start: 0.8338 (m) cc_final: 0.7755 (p) 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: 0.8444 (mm) REVERT: B 55 PHE cc_start: 0.7374 (m-80) cc_final: 0.7068 (m-80) REVERT: B 128 ILE cc_start: 0.8956 (mm) cc_final: 0.8612 (mm) REVERT: B 170 TYR cc_start: 0.8768 (t80) cc_final: 0.8325 (t80) REVERT: B 641 ASN cc_start: 0.7989 (m110) cc_final: 0.7630 (p0) REVERT: B 707 TYR cc_start: 0.8054 (t80) cc_final: 0.7273 (t80) REVERT: B 755 GLN cc_start: 0.8465 (tt0) cc_final: 0.8080 (tt0) 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: 0.7427 (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: 0.7592 (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: 0.1522 time to fit residues: 99.6310 Evaluate side-chains 304 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 207 HIS ** 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 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 777 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.204652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.112804 restraints weight = 51504.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116819 restraints weight = 21810.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119383 restraints weight = 12903.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121002 restraints weight = 9175.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.122043 restraints weight = 7361.224| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31473 Z= 0.205 Angle : 0.671 17.701 42957 Z= 0.336 Chirality : 0.048 0.427 4920 Planarity : 0.005 0.123 5481 Dihedral : 4.191 34.630 4182 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.94 % Allowed : 8.23 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 3825 helix: 1.00 (0.19), residues: 696 sheet: 0.59 (0.17), residues: 968 loop : -0.20 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 273 TYR 0.019 0.001 TYR A 204 PHE 0.024 0.002 PHE C 168 TRP 0.019 0.001 TRP A 886 HIS 0.012 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (31389) covalent geometry : angle 0.65022 / 0.33 (42747) SS BOND : bond 0.00642 / 0.40 ( 42) SS BOND : angle 1.07866 / 0.76 ( 84) hydrogen bonds : bond 0.04973 / 3.32 ( 1154) hydrogen bonds : angle 6.86463 / 4.80 ( 3111) link_NAG-ASN : bond 0.00618 / 0.41 ( 42) link_NAG-ASN : angle 3.07594 / 2.06 ( 126) *********************** 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 362 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 331 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7237 (t80) cc_final: 0.6793 (t80) REVERT: A 207 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7663 (m90) REVERT: A 584 ILE cc_start: 0.8683 (mm) cc_final: 0.8305 (mt) REVERT: A 610 VAL cc_start: 0.8998 (t) cc_final: 0.8689 (p) REVERT: A 756 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7560 (t80) REVERT: B 53 ASP cc_start: 0.8254 (t0) cc_final: 0.7673 (t70) REVERT: B 54 LEU cc_start: 0.8844 (mm) cc_final: 0.8291 (mm) REVERT: B 55 PHE cc_start: 0.7452 (m-80) cc_final: 0.7235 (m-10) REVERT: B 117 LEU cc_start: 0.8324 (tp) cc_final: 0.7968 (tt) REVERT: B 265 TYR cc_start: 0.5759 (p90) cc_final: 0.5480 (p90) REVERT: B 707 TYR cc_start: 0.8323 (t80) cc_final: 0.7426 (t80) REVERT: B 968 SER cc_start: 0.9021 (p) cc_final: 0.8804 (p) REVERT: B 970 PHE cc_start: 0.7743 (m-80) cc_final: 0.7131 (m-80) REVERT: B 1082 CYS cc_start: 0.6494 (t) cc_final: 0.6178 (t) REVERT: B 1139 ASP cc_start: 0.8222 (m-30) cc_final: 0.8006 (t0) REVERT: C 592 PHE cc_start: 0.8678 (p90) cc_final: 0.8440 (p90) REVERT: C 661 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 675 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 900 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.7083 (mtm) REVERT: C 1033 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8157 (p) REVERT: L 37 SER cc_start: 0.4067 (m) cc_final: 0.3815 (t) REVERT: P 21 MET cc_start: 0.2262 (tpt) cc_final: 0.1726 (tpt) REVERT: P 115 MET cc_start: 0.3341 (tpt) cc_final: 0.3137 (tpp) outliers start: 31 outliers final: 23 residues processed: 351 average time/residue: 0.1506 time to fit residues: 91.1135 Evaluate side-chains 324 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR 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 720 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 911 VAL 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 75 optimal weight: 2.9990 chunk 160 optimal weight: 0.0870 chunk 259 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 148 optimal weight: 50.0000 chunk 113 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 339 optimal weight: 0.0370 chunk 68 optimal weight: 0.5980 chunk 273 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 overall best weight: 0.7636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** 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 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 = 0.4623 r_free = 0.4623 target = 0.209323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118278 restraints weight = 51064.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124073 restraints weight = 22012.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125843 restraints weight = 10147.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126464 restraints weight = 7529.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126516 restraints weight = 7285.119| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1480 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= 0.116 Angle : 0.579 16.066 42957 Z= 0.286 Chirality : 0.046 0.365 4920 Planarity : 0.004 0.084 5481 Dihedral : 4.014 32.275 4182 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.06 % Allowed : 10.44 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 3825 helix: 1.27 (0.19), residues: 694 sheet: 0.62 (0.17), residues: 984 loop : -0.20 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.016 0.001 TYR B 160 PHE 0.026 0.001 PHE C 55 TRP 0.016 0.001 TRP C 64 HIS 0.015 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (31389) covalent geometry : angle 0.56215 / 0.28 (42747) SS BOND : bond 0.00190 / 0.13 ( 42) SS BOND : angle 1.03879 / 0.65 ( 84) hydrogen bonds : bond 0.04117 / 2.75 ( 1154) hydrogen bonds : angle 6.14693 / 4.29 ( 3111) link_NAG-ASN : bond 0.00542 / 0.38 ( 42) link_NAG-ASN : angle 2.53398 / 1.58 ( 126) *********************** 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 373 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 338 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8603 (t80) cc_final: 0.8207 (t80) REVERT: A 610 VAL cc_start: 0.9005 (t) cc_final: 0.8714 (p) REVERT: A 756 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 53 ASP cc_start: 0.8326 (t0) cc_final: 0.7714 (t70) REVERT: B 54 LEU cc_start: 0.8800 (mm) cc_final: 0.8225 (mm) REVERT: B 168 PHE cc_start: 0.7882 (t80) cc_final: 0.7576 (t80) REVERT: B 177 MET cc_start: 0.8531 (ppp) cc_final: 0.8281 (ppp) REVERT: B 214 ARG cc_start: 0.8474 (mpp-170) cc_final: 0.7103 (ttt-90) REVERT: B 265 TYR cc_start: 0.5483 (p90) cc_final: 0.5235 (p90) REVERT: B 587 ILE cc_start: 0.7724 (mt) cc_final: 0.7434 (mp) REVERT: B 707 TYR cc_start: 0.8168 (t80) cc_final: 0.7155 (t80) REVERT: B 730 SER cc_start: 0.8470 (t) cc_final: 0.8074 (p) REVERT: B 741 TYR cc_start: 0.8053 (t80) cc_final: 0.7720 (t80) REVERT: B 901 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 906 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: B 1082 CYS cc_start: 0.6270 (t) cc_final: 0.5983 (t) REVERT: B 1139 ASP cc_start: 0.8160 (m-30) cc_final: 0.7917 (t0) REVERT: C 176 LEU cc_start: 0.7055 (mm) cc_final: 0.6758 (mm) REVERT: C 196 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.6995 (t0) REVERT: C 584 ILE cc_start: 0.8088 (mm) cc_final: 0.7581 (mm) REVERT: C 587 ILE cc_start: 0.8981 (mt) cc_final: 0.8613 (tp) REVERT: C 592 PHE cc_start: 0.8675 (p90) cc_final: 0.8321 (p90) REVERT: C 661 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 675 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 731 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7090 (ptp) REVERT: L 37 SER cc_start: 0.4199 (m) cc_final: 0.3940 (t) outliers start: 35 outliers final: 16 residues processed: 360 average time/residue: 0.1463 time to fit residues: 90.3390 Evaluate side-chains 323 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 882 ILE 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 720 ILE Chi-restraints excluded: chain B residue 901 GLN 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 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 731 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 80 optimal weight: 0.0000 chunk 328 optimal weight: 50.0000 chunk 360 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 118 optimal weight: 30.0000 chunk 302 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 291 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.208494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.115700 restraints weight = 51140.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119880 restraints weight = 21239.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122534 restraints weight = 12424.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124177 restraints weight = 8813.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125186 restraints weight = 7128.598| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31473 Z= 0.111 Angle : 0.578 15.808 42957 Z= 0.283 Chirality : 0.046 0.366 4920 Planarity : 0.004 0.079 5481 Dihedral : 3.952 40.449 4182 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.36 % Allowed : 12.19 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 3825 helix: 1.32 (0.20), residues: 691 sheet: 0.61 (0.17), residues: 986 loop : -0.18 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.032 0.001 TYR A 873 PHE 0.021 0.001 PHE C 275 TRP 0.016 0.001 TRP A 886 HIS 0.016 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (31389) covalent geometry : angle 0.56029 / 0.28 (42747) SS BOND : bond 0.00307 / 0.22 ( 42) SS BOND : angle 1.50114 / 0.82 ( 84) hydrogen bonds : bond 0.03786 / 2.51 ( 1154) hydrogen bonds : angle 5.86019 / 4.09 ( 3111) link_NAG-ASN : bond 0.00531 / 0.36 ( 42) link_NAG-ASN : angle 2.41561 / 1.50 ( 126) *********************** 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 359 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8507 (t80) cc_final: 0.8129 (t80) REVERT: A 610 VAL cc_start: 0.8991 (t) cc_final: 0.8696 (p) REVERT: A 756 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.7604 (t80) REVERT: A 895 GLN cc_start: 0.7641 (pp30) cc_final: 0.7207 (pp30) REVERT: B 53 ASP cc_start: 0.8327 (t0) cc_final: 0.7879 (t70) REVERT: B 54 LEU cc_start: 0.8808 (mm) cc_final: 0.8534 (mm) REVERT: B 168 PHE cc_start: 0.7922 (t80) cc_final: 0.7602 (t80) REVERT: B 177 MET cc_start: 0.8477 (ppp) cc_final: 0.8272 (ppp) REVERT: B 214 ARG cc_start: 0.8396 (mpp-170) cc_final: 0.7007 (tmt170) REVERT: B 265 TYR cc_start: 0.5785 (p90) cc_final: 0.5478 (p90) REVERT: B 707 TYR cc_start: 0.8178 (t80) cc_final: 0.7398 (t80) REVERT: B 741 TYR cc_start: 0.8073 (t80) cc_final: 0.7777 (t80) REVERT: B 777 ASN cc_start: 0.8216 (m-40) cc_final: 0.7901 (m110) REVERT: B 901 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: B 906 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: B 1082 CYS cc_start: 0.6329 (t) cc_final: 0.5929 (t) REVERT: C 584 ILE cc_start: 0.8076 (mm) cc_final: 0.7578 (mm) REVERT: C 675 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7878 (tm-30) REVERT: C 731 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7149 (ptp) REVERT: L 37 SER cc_start: 0.4014 (m) cc_final: 0.3769 (t) REVERT: P 115 MET cc_start: 0.4451 (tpp) cc_final: 0.4054 (tpp) outliers start: 45 outliers final: 30 residues processed: 344 average time/residue: 0.1598 time to fit residues: 93.5483 Evaluate side-chains 322 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 596 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP 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 120 VAL Chi-restraints excluded: chain B residue 720 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 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 588 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET 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 30 optimal weight: 30.0000 chunk 189 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 48 optimal weight: 30.0000 chunk 76 optimal weight: 0.5980 chunk 153 optimal weight: 0.1980 chunk 291 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 194 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 856 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 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 = 0.4634 r_free = 0.4634 target = 0.209815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118370 restraints weight = 51155.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122702 restraints weight = 21003.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125432 restraints weight = 12165.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127200 restraints weight = 8548.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128316 restraints weight = 6827.970| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31473 Z= 0.101 Angle : 0.557 15.017 42957 Z= 0.274 Chirality : 0.045 0.339 4920 Planarity : 0.004 0.066 5481 Dihedral : 3.865 29.333 4182 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.48 % Allowed : 12.98 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3825 helix: 1.41 (0.20), residues: 688 sheet: 0.65 (0.17), residues: 970 loop : -0.18 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 237 TYR 0.022 0.001 TYR A 873 PHE 0.027 0.001 PHE C 275 TRP 0.015 0.001 TRP A 886 HIS 0.013 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (31389) covalent geometry : angle 0.54149 / 0.27 (42747) SS BOND : bond 0.00495 / 0.35 ( 42) SS BOND : angle 1.04755 / 0.71 ( 84) hydrogen bonds : bond 0.03565 / 2.38 ( 1154) hydrogen bonds : angle 5.58895 / 3.90 ( 3111) link_NAG-ASN : bond 0.00537 / 0.37 ( 42) link_NAG-ASN : angle 2.33536 / 1.45 ( 126) *********************** 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 373 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 324 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7191 (t80) cc_final: 0.6985 (t80) REVERT: A 215 ASP cc_start: 0.7440 (m-30) cc_final: 0.6887 (p0) REVERT: A 318 PHE cc_start: 0.8514 (t80) cc_final: 0.8144 (t80) REVERT: A 610 VAL cc_start: 0.8975 (t) cc_final: 0.8676 (p) REVERT: A 756 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.7595 (t80) REVERT: A 895 GLN cc_start: 0.7596 (pp30) cc_final: 0.7333 (pp30) REVERT: B 168 PHE cc_start: 0.7935 (t80) cc_final: 0.7689 (t80) REVERT: B 201 PHE cc_start: 0.6744 (t80) cc_final: 0.6504 (t80) REVERT: B 228 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7134 (t70) REVERT: B 265 TYR cc_start: 0.5875 (p90) cc_final: 0.5582 (p90) REVERT: B 697 MET cc_start: 0.8034 (ttm) cc_final: 0.7813 (ttt) REVERT: B 707 TYR cc_start: 0.8129 (t80) cc_final: 0.7361 (t80) REVERT: B 741 TYR cc_start: 0.8064 (t80) cc_final: 0.7796 (t80) REVERT: B 856 ASN cc_start: 0.6468 (t0) cc_final: 0.6002 (m110) REVERT: B 901 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: B 906 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: B 1082 CYS cc_start: 0.6268 (t) cc_final: 0.5930 (t) REVERT: C 38 TYR cc_start: 0.7841 (m-80) cc_final: 0.7481 (m-80) REVERT: C 196 ASN cc_start: 0.7561 (p0) cc_final: 0.6606 (t0) REVERT: C 584 ILE cc_start: 0.8047 (mm) cc_final: 0.7553 (mm) REVERT: C 592 PHE cc_start: 0.8421 (p90) cc_final: 0.8026 (p90) REVERT: C 675 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 699 LEU cc_start: 0.8028 (tp) cc_final: 0.7522 (mt) REVERT: C 731 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7144 (ptp) REVERT: C 1028 LYS cc_start: 0.7113 (mmtm) cc_final: 0.6864 (tppt) REVERT: L 37 SER cc_start: 0.4075 (m) cc_final: 0.3810 (t) REVERT: P 115 MET cc_start: 0.4848 (tpp) cc_final: 0.4447 (tpp) outliers start: 49 outliers final: 31 residues processed: 354 average time/residue: 0.1438 time to fit residues: 88.8134 Evaluate side-chains 329 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 560 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 886 TRP 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 B residue 120 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 794 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 1008 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE 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 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 1066 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 101 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 371 optimal weight: 50.0000 chunk 299 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 218 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** ** B 895 GLN ** 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 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 = 0.4544 r_free = 0.4544 target = 0.205161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113248 restraints weight = 51751.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118192 restraints weight = 22680.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119862 restraints weight = 12077.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121336 restraints weight = 8103.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.121434 restraints weight = 7012.547| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31473 Z= 0.136 Angle : 0.574 15.762 42957 Z= 0.283 Chirality : 0.046 0.349 4920 Planarity : 0.004 0.065 5481 Dihedral : 3.895 27.621 4182 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.97 % Allowed : 14.13 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3825 helix: 1.32 (0.20), residues: 688 sheet: 0.60 (0.17), residues: 985 loop : -0.17 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.018 0.001 TYR A 873 PHE 0.029 0.001 PHE C 275 TRP 0.017 0.001 TRP A 886 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (31389) covalent geometry : angle 0.55767 / 0.28 (42747) SS BOND : bond 0.00275 / 0.19 ( 42) SS BOND : angle 1.22391 / 0.76 ( 84) hydrogen bonds : bond 0.03655 / 2.42 ( 1154) hydrogen bonds : angle 5.54063 / 3.86 ( 3111) link_NAG-ASN : bond 0.00519 / 0.35 ( 42) link_NAG-ASN : angle 2.40391 / 1.50 ( 126) *********************** 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 367 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7160 (m90) REVERT: A 215 ASP cc_start: 0.7349 (m-30) cc_final: 0.6795 (p0) REVERT: A 271 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7741 (mp10) REVERT: A 306 PHE cc_start: 0.6782 (m-80) cc_final: 0.6434 (m-80) REVERT: A 318 PHE cc_start: 0.8523 (t80) cc_final: 0.8164 (t80) REVERT: A 610 VAL cc_start: 0.8938 (t) cc_final: 0.8615 (p) REVERT: A 756 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.7668 (t80) REVERT: A 895 GLN cc_start: 0.7642 (pp30) cc_final: 0.7300 (pp30) REVERT: B 53 ASP cc_start: 0.8194 (t0) cc_final: 0.7736 (t70) REVERT: B 54 LEU cc_start: 0.8897 (mt) cc_final: 0.8670 (mm) REVERT: B 168 PHE cc_start: 0.8038 (t80) cc_final: 0.7772 (t80) REVERT: B 214 ARG cc_start: 0.8512 (mpp-170) cc_final: 0.7023 (tmt170) REVERT: B 228 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7241 (t70) REVERT: B 265 TYR cc_start: 0.5350 (p90) cc_final: 0.5094 (p90) REVERT: B 607 GLN cc_start: 0.8584 (mt0) cc_final: 0.8372 (tt0) REVERT: B 697 MET cc_start: 0.8293 (ttm) cc_final: 0.7971 (ttt) REVERT: B 707 TYR cc_start: 0.8320 (t80) cc_final: 0.7273 (t80) REVERT: B 731 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7705 (ptm) REVERT: B 741 TYR cc_start: 0.7955 (t80) cc_final: 0.7740 (t80) REVERT: B 901 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: B 906 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: B 1082 CYS cc_start: 0.6371 (t) cc_final: 0.5998 (t) REVERT: C 38 TYR cc_start: 0.8048 (m-80) cc_final: 0.7456 (m-80) REVERT: C 196 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6544 (t0) REVERT: C 197 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8397 (mp) REVERT: C 584 ILE cc_start: 0.8050 (mm) cc_final: 0.7529 (mm) REVERT: C 675 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7819 (tm-30) REVERT: C 731 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7378 (ptp) REVERT: C 1033 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8142 (p) REVERT: L 37 SER cc_start: 0.4140 (m) cc_final: 0.3875 (t) REVERT: P 115 MET cc_start: 0.5132 (tpp) cc_final: 0.4677 (tpp) outliers start: 65 outliers final: 44 residues processed: 341 average time/residue: 0.1511 time to fit residues: 88.9530 Evaluate side-chains 339 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 973 ILE 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 B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 794 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 1008 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 197 ILE 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 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 787 GLN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 38 optimal weight: 8.9990 chunk 182 optimal weight: 0.0060 chunk 205 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 100 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 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** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.209257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117284 restraints weight = 51545.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122655 restraints weight = 22674.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124640 restraints weight = 12052.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125539 restraints weight = 8126.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125878 restraints weight = 7787.218| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31473 Z= 0.132 Angle : 0.575 15.411 42957 Z= 0.284 Chirality : 0.046 0.359 4920 Planarity : 0.004 0.065 5481 Dihedral : 3.888 26.434 4182 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 14.10 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3825 helix: 1.30 (0.19), residues: 689 sheet: 0.59 (0.17), residues: 989 loop : -0.18 (0.14), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.021 0.001 TYR A 873 PHE 0.021 0.001 PHE C 135 TRP 0.016 0.001 TRP A 886 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (31389) covalent geometry : angle 0.55869 / 0.28 (42747) SS BOND : bond 0.00353 / 0.21 ( 42) SS BOND : angle 1.23722 / 0.73 ( 84) hydrogen bonds : bond 0.03605 / 2.39 ( 1154) hydrogen bonds : angle 5.49502 / 3.83 ( 3111) link_NAG-ASN : bond 0.00516 / 0.35 ( 42) link_NAG-ASN : angle 2.38794 / 1.48 ( 126) *********************** 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 374 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 298 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7383 (m-30) cc_final: 0.6768 (p0) REVERT: A 271 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7788 (mp10) REVERT: A 306 PHE cc_start: 0.6705 (m-80) cc_final: 0.6404 (m-80) REVERT: A 318 PHE cc_start: 0.8520 (t80) cc_final: 0.8175 (t80) REVERT: A 610 VAL cc_start: 0.8990 (t) cc_final: 0.8678 (p) REVERT: A 675 GLN cc_start: 0.7970 (tp40) cc_final: 0.7707 (mm-40) REVERT: A 699 LEU cc_start: 0.7940 (tt) cc_final: 0.7421 (tt) REVERT: A 756 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.7697 (t80) REVERT: A 895 GLN cc_start: 0.7710 (pp30) cc_final: 0.7244 (pp30) REVERT: B 53 ASP cc_start: 0.8203 (t0) cc_final: 0.7683 (t70) REVERT: B 54 LEU cc_start: 0.8895 (mt) cc_final: 0.8629 (mm) REVERT: B 168 PHE cc_start: 0.8081 (t80) cc_final: 0.7874 (t80) REVERT: B 214 ARG cc_start: 0.8496 (mpp-170) cc_final: 0.7108 (tmt170) REVERT: B 228 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7389 (t70) REVERT: B 265 TYR cc_start: 0.5452 (p90) cc_final: 0.5209 (p90) REVERT: B 697 MET cc_start: 0.8357 (ttm) cc_final: 0.8018 (ttt) REVERT: B 707 TYR cc_start: 0.8316 (t80) cc_final: 0.7261 (t80) REVERT: B 856 ASN cc_start: 0.6523 (t0) cc_final: 0.5990 (m110) REVERT: B 873 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 901 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: B 906 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: B 1082 CYS cc_start: 0.6371 (t) cc_final: 0.5996 (t) REVERT: C 38 TYR cc_start: 0.8151 (m-80) cc_final: 0.7498 (m-80) REVERT: C 533 LEU cc_start: 0.8125 (mt) cc_final: 0.7915 (mt) REVERT: C 584 ILE cc_start: 0.8052 (mm) cc_final: 0.7529 (mm) REVERT: C 675 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 697 MET cc_start: 0.8921 (mmt) cc_final: 0.8570 (mmt) REVERT: C 731 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7455 (ptp) REVERT: C 1033 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (p) REVERT: L 37 SER cc_start: 0.4173 (m) cc_final: 0.3906 (t) REVERT: P 115 MET cc_start: 0.5079 (tpp) cc_final: 0.4616 (tpp) outliers start: 76 outliers final: 53 residues processed: 348 average time/residue: 0.1568 time to fit residues: 93.9284 Evaluate side-chains 339 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 238 PHE 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 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 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 193 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 361 CYS 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 794 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 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1008 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 105 ILE 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 551 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 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE 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 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 151 optimal weight: 8.9990 chunk 222 optimal weight: 40.0000 chunk 138 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 371 optimal weight: 40.0000 chunk 120 optimal weight: 1.9990 chunk 363 optimal weight: 40.0000 chunk 282 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** 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** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.206628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111894 restraints weight = 51822.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116058 restraints weight = 22396.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118669 restraints weight = 13310.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120419 restraints weight = 9516.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121493 restraints weight = 7635.382| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31473 Z= 0.152 Angle : 0.592 16.328 42957 Z= 0.293 Chirality : 0.046 0.369 4920 Planarity : 0.004 0.082 5481 Dihedral : 3.950 25.226 4182 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.33 % Allowed : 14.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3825 helix: 1.30 (0.20), residues: 676 sheet: 0.61 (0.17), residues: 980 loop : -0.23 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.022 0.001 TYR C 873 PHE 0.034 0.002 PHE C 135 TRP 0.017 0.001 TRP A 886 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (31389) covalent geometry : angle 0.57608 / 0.29 (42747) SS BOND : bond 0.00280 / 0.19 ( 42) SS BOND : angle 1.18453 / 0.80 ( 84) hydrogen bonds : bond 0.03687 / 2.43 ( 1154) hydrogen bonds : angle 5.48836 / 3.83 ( 3111) link_NAG-ASN : bond 0.00515 / 0.35 ( 42) link_NAG-ASN : angle 2.43270 / 1.49 ( 126) *********************** 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 360 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7427 (m-30) cc_final: 0.6805 (p0) REVERT: A 271 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7921 (mp10) REVERT: A 318 PHE cc_start: 0.8495 (t80) cc_final: 0.8181 (t80) REVERT: A 610 VAL cc_start: 0.9040 (t) cc_final: 0.8751 (p) REVERT: A 675 GLN cc_start: 0.8075 (tp40) cc_final: 0.7787 (mm-40) REVERT: A 756 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7735 (t80) REVERT: A 895 GLN cc_start: 0.7760 (pp30) cc_final: 0.7220 (pp30) REVERT: B 53 ASP cc_start: 0.8203 (t0) cc_final: 0.7673 (t70) REVERT: B 54 LEU cc_start: 0.8916 (mt) cc_final: 0.8664 (mm) REVERT: B 168 PHE cc_start: 0.8126 (t80) cc_final: 0.7917 (t80) REVERT: B 214 ARG cc_start: 0.8457 (mpp-170) cc_final: 0.7159 (tmt170) REVERT: B 265 TYR cc_start: 0.5782 (p90) cc_final: 0.5475 (p90) REVERT: B 707 TYR cc_start: 0.8316 (t80) cc_final: 0.7244 (t80) REVERT: B 731 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7689 (ptm) REVERT: B 873 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7322 (t80) REVERT: B 901 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: B 906 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: B 943 SER cc_start: 0.8388 (m) cc_final: 0.8105 (p) REVERT: B 1082 CYS cc_start: 0.6420 (t) cc_final: 0.6034 (t) REVERT: C 38 TYR cc_start: 0.8099 (m-80) cc_final: 0.7451 (m-80) REVERT: C 584 ILE cc_start: 0.8078 (mm) cc_final: 0.7557 (mm) REVERT: C 697 MET cc_start: 0.8922 (mmt) cc_final: 0.8611 (mmt) REVERT: C 731 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7335 (ptp) REVERT: C 1050 MET cc_start: 0.6130 (ttm) cc_final: 0.5687 (ttp) REVERT: L 37 SER cc_start: 0.4055 (m) cc_final: 0.3805 (t) REVERT: P 115 MET cc_start: 0.5416 (tpp) cc_final: 0.4921 (tpp) outliers start: 77 outliers final: 59 residues processed: 336 average time/residue: 0.1532 time to fit residues: 88.6985 Evaluate side-chains 340 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 238 PHE 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 864 LEU 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 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 B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR 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 641 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 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 938 LEU Chi-restraints excluded: chain B residue 968 SER 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 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 551 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 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE 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 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 311 optimal weight: 0.7980 chunk 182 optimal weight: 0.0570 chunk 261 optimal weight: 8.9990 chunk 293 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 314 optimal weight: 0.0470 chunk 233 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 221 optimal weight: 4.9990 chunk 340 optimal weight: 50.0000 chunk 236 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 218 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** ** B1048 HIS ** 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 = 0.4561 r_free = 0.4561 target = 0.206775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115108 restraints weight = 51751.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120194 restraints weight = 22784.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122145 restraints weight = 12194.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123271 restraints weight = 8387.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123606 restraints weight = 7891.363| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31473 Z= 0.102 Angle : 0.567 14.953 42957 Z= 0.277 Chirality : 0.046 0.362 4920 Planarity : 0.004 0.061 5481 Dihedral : 3.805 23.665 4182 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.66 % Allowed : 15.46 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3825 helix: 1.45 (0.20), residues: 677 sheet: 0.70 (0.17), residues: 975 loop : -0.19 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.022 0.001 TYR A 170 PHE 0.057 0.001 PHE A 135 TRP 0.015 0.001 TRP A 886 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (31389) covalent geometry : angle 0.55098 / 0.27 (42747) SS BOND : bond 0.00386 / 0.25 ( 42) SS BOND : angle 1.26373 / 0.85 ( 84) hydrogen bonds : bond 0.03414 / 2.26 ( 1154) hydrogen bonds : angle 5.26848 / 3.66 ( 3111) link_NAG-ASN : bond 0.00545 / 0.37 ( 42) link_NAG-ASN : angle 2.34247 / 1.45 ( 126) *********************** 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 369 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.6977 (m90) REVERT: A 215 ASP cc_start: 0.7349 (m-30) cc_final: 0.6777 (p0) REVERT: A 271 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7840 (mp10) REVERT: A 610 VAL cc_start: 0.8888 (t) cc_final: 0.8583 (p) REVERT: A 675 GLN cc_start: 0.7932 (tp40) cc_final: 0.7682 (mm-40) REVERT: A 699 LEU cc_start: 0.7885 (tt) cc_final: 0.7489 (tt) REVERT: A 756 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 895 GLN cc_start: 0.7803 (pp30) cc_final: 0.7240 (pp30) REVERT: B 53 ASP cc_start: 0.8105 (t0) cc_final: 0.7578 (t70) REVERT: B 54 LEU cc_start: 0.8920 (mt) cc_final: 0.8677 (mm) REVERT: B 81 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8064 (t0) REVERT: B 168 PHE cc_start: 0.8066 (t80) cc_final: 0.7840 (t80) REVERT: B 177 MET cc_start: 0.8841 (ppp) cc_final: 0.8373 (ppp) REVERT: B 214 ARG cc_start: 0.8493 (mpp-170) cc_final: 0.7142 (tmt170) REVERT: B 276 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 641 ASN cc_start: 0.8201 (m110) cc_final: 0.7687 (p0) REVERT: B 707 TYR cc_start: 0.8161 (t80) cc_final: 0.7350 (t80) REVERT: B 731 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7585 (ptm) REVERT: B 856 ASN cc_start: 0.6444 (t0) cc_final: 0.5886 (m110) REVERT: B 873 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7258 (t80) REVERT: B 901 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: B 902 MET cc_start: 0.7870 (tpp) cc_final: 0.7530 (tpp) REVERT: B 906 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: B 943 SER cc_start: 0.8390 (m) cc_final: 0.8123 (p) REVERT: B 1082 CYS cc_start: 0.6301 (t) cc_final: 0.5903 (t) REVERT: C 38 TYR cc_start: 0.8032 (m-80) cc_final: 0.7371 (m-80) REVERT: C 110 LEU cc_start: 0.8640 (tp) cc_final: 0.8326 (mp) REVERT: C 177 MET cc_start: 0.6998 (mtt) cc_final: 0.6772 (tpt) REVERT: C 584 ILE cc_start: 0.8001 (mm) cc_final: 0.7473 (mm) REVERT: C 697 MET cc_start: 0.8960 (mmt) cc_final: 0.8731 (mmt) REVERT: C 731 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7319 (ptp) REVERT: C 1028 LYS cc_start: 0.7267 (mmtm) cc_final: 0.7031 (tppt) REVERT: L 37 SER cc_start: 0.4166 (m) cc_final: 0.3894 (t) REVERT: P 115 MET cc_start: 0.5277 (tpp) cc_final: 0.4750 (tpp) outliers start: 55 outliers final: 41 residues processed: 351 average time/residue: 0.1631 time to fit residues: 97.6210 Evaluate side-chains 332 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 223 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 864 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 976 VAL 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 B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET 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 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1050 MET 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 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 731 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 34 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 33 optimal weight: 40.0000 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.207528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113157 restraints weight = 51874.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117184 restraints weight = 22584.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119784 restraints weight = 13465.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121512 restraints weight = 9611.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122621 restraints weight = 7751.080| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31473 Z= 0.167 Angle : 0.605 13.813 42957 Z= 0.300 Chirality : 0.046 0.372 4920 Planarity : 0.004 0.079 5481 Dihedral : 3.941 23.372 4182 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.72 % Allowed : 16.15 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3825 helix: 1.37 (0.20), residues: 671 sheet: 0.64 (0.17), residues: 977 loop : -0.25 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1039 TYR 0.027 0.001 TYR C 873 PHE 0.033 0.002 PHE A 135 TRP 0.018 0.001 TRP A 886 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (31389) covalent geometry : angle 0.58876 / 0.30 (42747) SS BOND : bond 0.00311 / 0.20 ( 42) SS BOND : angle 1.36996 / 0.94 ( 84) hydrogen bonds : bond 0.03670 / 2.43 ( 1154) hydrogen bonds : angle 5.38704 / 3.75 ( 3111) link_NAG-ASN : bond 0.00514 / 0.35 ( 42) link_NAG-ASN : angle 2.41145 / 1.48 ( 126) ********************** 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 336 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7306 (m90) REVERT: A 271 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7997 (mp10) REVERT: A 610 VAL cc_start: 0.9028 (t) cc_final: 0.8749 (p) REVERT: A 675 GLN cc_start: 0.8086 (tp40) cc_final: 0.7812 (mm-40) REVERT: A 756 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.7778 (t80) REVERT: A 895 GLN cc_start: 0.7833 (pp30) cc_final: 0.7178 (pp30) REVERT: A 957 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 53 ASP cc_start: 0.8197 (t0) cc_final: 0.7631 (t70) REVERT: B 54 LEU cc_start: 0.8946 (mt) cc_final: 0.8741 (mm) REVERT: B 55 PHE cc_start: 0.6513 (m-10) cc_final: 0.6284 (m-10) REVERT: B 168 PHE cc_start: 0.7967 (t80) cc_final: 0.7762 (t80) REVERT: B 177 MET cc_start: 0.8877 (ppp) cc_final: 0.8366 (ppp) REVERT: B 214 ARG cc_start: 0.8440 (mpp-170) cc_final: 0.7262 (tpt170) REVERT: B 276 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8176 (mm) REVERT: B 697 MET cc_start: 0.8670 (tpp) cc_final: 0.8200 (mmt) REVERT: B 707 TYR cc_start: 0.8331 (t80) cc_final: 0.7413 (t80) REVERT: B 856 ASN cc_start: 0.6413 (t0) cc_final: 0.5746 (m110) REVERT: B 873 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 901 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 906 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: B 943 SER cc_start: 0.8380 (m) cc_final: 0.8121 (p) REVERT: B 1082 CYS cc_start: 0.6455 (t) cc_final: 0.6067 (t) REVERT: C 38 TYR cc_start: 0.8166 (m-80) cc_final: 0.7582 (m-80) REVERT: C 110 LEU cc_start: 0.8634 (tp) cc_final: 0.8301 (mp) REVERT: C 177 MET cc_start: 0.6954 (mtt) cc_final: 0.6752 (tpt) REVERT: C 584 ILE cc_start: 0.8134 (mm) cc_final: 0.7624 (mm) REVERT: C 697 MET cc_start: 0.8963 (mmt) cc_final: 0.8182 (mmt) REVERT: C 731 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7322 (ptp) REVERT: C 823 PHE cc_start: 0.8077 (t80) cc_final: 0.7741 (t80) REVERT: C 984 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7623 (tp) REVERT: C 1028 LYS cc_start: 0.7097 (mmtm) cc_final: 0.6801 (tppt) REVERT: C 1033 VAL cc_start: 0.8540 (t) cc_final: 0.8222 (p) REVERT: L 37 SER cc_start: 0.4058 (m) cc_final: 0.3802 (t) REVERT: P 115 MET cc_start: 0.5379 (tpp) cc_final: 0.4831 (tpp) outliers start: 57 outliers final: 47 residues processed: 319 average time/residue: 0.1815 time to fit residues: 98.5714 Evaluate side-chains 323 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 223 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 864 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR 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 B residue 120 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL 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 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 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 656 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 787 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 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 98 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 364 optimal weight: 50.0000 chunk 239 optimal weight: 0.9990 chunk 284 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** 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 ** B1048 HIS ** 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 = 0.4556 r_free = 0.4556 target = 0.209342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116227 restraints weight = 51921.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120471 restraints weight = 21959.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123189 restraints weight = 12872.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124945 restraints weight = 9114.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126048 restraints weight = 7315.540| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31473 Z= 0.108 Angle : 0.572 13.337 42957 Z= 0.280 Chirality : 0.046 0.366 4920 Planarity : 0.004 0.074 5481 Dihedral : 3.830 22.796 4182 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.60 % Allowed : 16.30 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3825 helix: 1.47 (0.20), residues: 677 sheet: 0.65 (0.17), residues: 984 loop : -0.23 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.020 0.001 TYR B 160 PHE 0.031 0.001 PHE C 135 TRP 0.013 0.001 TRP A 886 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (31389) covalent geometry : angle 0.55686 / 0.28 (42747) SS BOND : bond 0.00208 / 0.14 ( 42) SS BOND : angle 1.20382 / 0.82 ( 84) hydrogen bonds : bond 0.03415 / 2.27 ( 1154) hydrogen bonds : angle 5.21474 / 3.63 ( 3111) link_NAG-ASN : bond 0.00528 / 0.36 ( 42) link_NAG-ASN : angle 2.35282 / 1.44 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7484.98 seconds wall clock time: 128 minutes 56.98 seconds (7736.98 seconds total)