Starting phenix.real_space_refine on Fri Mar 6 12:12:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz9_26883/03_2026/7uz9_26883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz9_26883/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz9_26883/03_2026/7uz9_26883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz9_26883/03_2026/7uz9_26883.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz9_26883/03_2026/7uz9_26883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz9_26883/03_2026/7uz9_26883.cif" } 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-5986/lib/python3.9/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 dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 6.72, per 1000 atoms: 0.22 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: 2.67 Conformation dependent library (CDL) restraints added in 1.2 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: 1.42 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: 7.64 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9800 1.35 - 1.47: 7960 1.47 - 1.59: 13458 1.59 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 31389 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 ... (remaining 31384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 42101 2.10 - 4.19: 593 4.19 - 6.29: 39 6.29 - 8.38: 9 8.38 - 10.48: 5 Bond angle restraints: 42747 Sorted by residual: angle pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " pdb=" NE ARG B 273 " ideal model delta sigma weight residual 112.00 101.83 10.17 2.20e+00 2.07e-01 2.14e+01 angle pdb=" N VAL M 111A" pdb=" CA VAL M 111A" pdb=" C VAL M 111A" ideal model delta sigma weight residual 112.98 109.16 3.82 1.25e+00 6.40e-01 9.36e+00 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.71 110.93 2.78 9.50e-01 1.11e+00 8.58e+00 angle pdb=" C TYR H 112 " pdb=" CA TYR H 112 " pdb=" CB TYR H 112 " ideal model delta sigma weight residual 110.42 116.03 -5.61 1.99e+00 2.53e-01 7.94e+00 ... (remaining 42742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 18026 23.09 - 46.18: 912 46.18 - 69.27: 95 69.27 - 92.37: 43 92.37 - 115.46: 76 Dihedral angle restraints: 19152 sinusoidal: 7896 harmonic: 11256 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 7.45 85.55 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 104 " pdb=" CB CYS P 104 " ideal model delta sinusoidal sigma weight residual 93.00 36.09 56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA TRP A 886 " pdb=" C TRP A 886 " pdb=" N THR A 887 " pdb=" CA THR A 887 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 19149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4703 0.099 - 0.198: 206 0.198 - 0.297: 9 0.297 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4917 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 273 " 0.398 9.50e-02 1.11e+02 1.78e-01 2.01e+01 pdb=" NE ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 273 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 273 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 579 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO C 85 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1267 2.72 - 3.27: 30860 3.27 - 3.81: 49793 3.81 - 4.36: 58865 4.36 - 4.90: 99897 Nonbonded interactions: 240682 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.175 3.040 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.188 3.040 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.188 3.120 nonbonded pdb=" O MET C 731 " pdb=" NE2 GLN C 774 " model vdw 2.197 3.120 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.200 3.040 ... (remaining 240677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.110 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31473 Z= 0.165 Angle : 0.608 10.480 42957 Z= 0.310 Chirality : 0.045 0.494 4920 Planarity : 0.005 0.178 5481 Dihedral : 15.469 115.458 11820 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.63 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 covalent geometry : bond 0.00344 (31389) covalent geometry : angle 0.58974 (42747) SS BOND : bond 0.00209 ( 42) SS BOND : angle 0.95912 ( 84) hydrogen bonds : bond 0.23873 ( 1154) hydrogen bonds : angle 8.83553 ( 3111) link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 2.68737 ( 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 : 0.980 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: 0.1611 time to fit residues: 105.8455 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 : 1.250 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.204712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.112533 restraints weight = 51622.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116527 restraints weight = 21947.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119119 restraints weight = 13014.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120730 restraints weight = 9254.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121781 restraints weight = 7443.836| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1206 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= 0.203 Angle : 0.695 17.928 42957 Z= 0.341 Chirality : 0.049 0.397 4920 Planarity : 0.005 0.121 5481 Dihedral : 11.647 113.280 5064 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.97 % Allowed : 8.32 % Favored : 90.71 % 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: 0.99 (0.19), residues: 696 sheet: 0.60 (0.17), residues: 972 loop : -0.21 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 273 TYR 0.019 0.002 TYR A 204 PHE 0.025 0.002 PHE C 168 TRP 0.017 0.001 TRP A 886 HIS 0.013 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00460 (31389) covalent geometry : angle 0.67287 (42747) SS BOND : bond 0.00282 ( 42) SS BOND : angle 1.07379 ( 84) hydrogen bonds : bond 0.04963 ( 1154) hydrogen bonds : angle 6.84966 ( 3111) link_NAG-ASN : bond 0.00582 ( 42) link_NAG-ASN : angle 3.18266 ( 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: 32 poor density : 330 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7219 (t80) cc_final: 0.6765 (t80) REVERT: A 207 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7662 (m90) REVERT: A 584 ILE cc_start: 0.8676 (mm) cc_final: 0.8298 (mt) REVERT: A 610 VAL cc_start: 0.8999 (t) cc_final: 0.8689 (p) REVERT: A 756 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7562 (t80) REVERT: B 53 ASP cc_start: 0.8258 (t0) cc_final: 0.7723 (t70) REVERT: B 54 LEU cc_start: 0.8848 (mm) cc_final: 0.8463 (mm) REVERT: B 55 PHE cc_start: 0.7457 (m-80) cc_final: 0.7183 (m-80) REVERT: B 117 LEU cc_start: 0.8313 (tp) cc_final: 0.7951 (tt) REVERT: B 265 TYR cc_start: 0.5757 (p90) cc_final: 0.5479 (p90) REVERT: B 707 TYR cc_start: 0.8323 (t80) cc_final: 0.7426 (t80) REVERT: B 741 TYR cc_start: 0.8127 (t80) cc_final: 0.7850 (t80) REVERT: B 968 SER cc_start: 0.9021 (p) cc_final: 0.8805 (p) REVERT: B 970 PHE cc_start: 0.7751 (m-80) cc_final: 0.7132 (m-80) REVERT: B 1082 CYS cc_start: 0.6492 (t) cc_final: 0.6175 (t) REVERT: B 1139 ASP cc_start: 0.8220 (m-30) cc_final: 0.8002 (t0) REVERT: C 592 PHE cc_start: 0.8683 (p90) cc_final: 0.8462 (p90) REVERT: C 661 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 675 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 900 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.7090 (mtm) REVERT: C 1033 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8159 (p) REVERT: L 37 SER cc_start: 0.4039 (m) cc_final: 0.3788 (t) REVERT: P 21 MET cc_start: 0.2286 (tpt) cc_final: 0.1740 (tpt) outliers start: 32 outliers final: 24 residues processed: 350 average time/residue: 0.1588 time to fit residues: 96.0175 Evaluate side-chains 323 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 976 VAL 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: 0.9980 chunk 259 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 148 optimal weight: 50.0000 chunk 113 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 339 optimal weight: 50.0000 chunk 68 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 74 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 563 GLN ** 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 = 0.4626 r_free = 0.4626 target = 0.210232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117856 restraints weight = 51004.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122093 restraints weight = 21060.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124841 restraints weight = 12283.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126510 restraints weight = 8662.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127574 restraints weight = 6938.495| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1496 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= 0.115 Angle : 0.597 16.047 42957 Z= 0.290 Chirality : 0.046 0.344 4920 Planarity : 0.004 0.084 5481 Dihedral : 8.874 118.422 5064 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.06 % Allowed : 10.56 % Favored : 88.38 % 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: 1.26 (0.19), residues: 695 sheet: 0.64 (0.17), residues: 994 loop : -0.20 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1039 TYR 0.016 0.001 TYR B 369 PHE 0.026 0.001 PHE C 55 TRP 0.015 0.001 TRP A 886 HIS 0.015 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00254 (31389) covalent geometry : angle 0.57962 (42747) SS BOND : bond 0.00208 ( 42) SS BOND : angle 1.06959 ( 84) hydrogen bonds : bond 0.04139 ( 1154) hydrogen bonds : angle 6.14566 ( 3111) link_NAG-ASN : bond 0.00547 ( 42) link_NAG-ASN : angle 2.60992 ( 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 374 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 339 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8601 (t80) cc_final: 0.8204 (t80) REVERT: A 596 SER cc_start: 0.8280 (m) cc_final: 0.7839 (p) REVERT: A 610 VAL cc_start: 0.8996 (t) cc_final: 0.8690 (p) REVERT: A 756 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7567 (t80) REVERT: B 53 ASP cc_start: 0.8309 (t0) cc_final: 0.7707 (t70) REVERT: B 54 LEU cc_start: 0.8838 (mm) cc_final: 0.8428 (mm) REVERT: B 168 PHE cc_start: 0.7823 (t80) cc_final: 0.7532 (t80) REVERT: B 177 MET cc_start: 0.8505 (ppp) cc_final: 0.8239 (ppp) REVERT: B 214 ARG cc_start: 0.8400 (mpp-170) cc_final: 0.7076 (ttt-90) REVERT: B 265 TYR cc_start: 0.5791 (p90) cc_final: 0.5550 (p90) REVERT: B 587 ILE cc_start: 0.7714 (mt) cc_final: 0.7425 (mp) REVERT: B 707 TYR cc_start: 0.8163 (t80) cc_final: 0.7360 (t80) REVERT: B 730 SER cc_start: 0.8465 (t) cc_final: 0.8068 (p) REVERT: B 741 TYR cc_start: 0.8062 (t80) cc_final: 0.7720 (t80) REVERT: B 901 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: B 906 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: B 1082 CYS cc_start: 0.6306 (t) cc_final: 0.6016 (t) REVERT: B 1139 ASP cc_start: 0.8180 (m-30) cc_final: 0.7974 (t0) REVERT: C 176 LEU cc_start: 0.7128 (mm) cc_final: 0.6838 (mm) REVERT: C 196 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6988 (t0) REVERT: C 584 ILE cc_start: 0.8083 (mm) cc_final: 0.7579 (mm) REVERT: C 587 ILE cc_start: 0.8967 (mt) cc_final: 0.8604 (tp) REVERT: C 592 PHE cc_start: 0.8700 (p90) cc_final: 0.8349 (p90) REVERT: C 658 ASN cc_start: 0.8232 (t0) cc_final: 0.7589 (t0) REVERT: C 661 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7750 (tm-30) REVERT: C 675 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7829 (tm-30) REVERT: C 731 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7174 (ptp) REVERT: L 37 SER cc_start: 0.4089 (m) cc_final: 0.3833 (t) REVERT: P 115 MET cc_start: 0.4444 (tpp) cc_final: 0.4015 (tpp) outliers start: 35 outliers final: 16 residues processed: 360 average time/residue: 0.1563 time to fit residues: 97.1507 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 : 1.060 ------------------------------------------------------------------------------- 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: 1.9990 chunk 328 optimal weight: 40.0000 chunk 360 optimal weight: 40.0000 chunk 114 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 302 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.205070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109904 restraints weight = 51864.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114072 restraints weight = 22245.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116729 restraints weight = 13261.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118337 restraints weight = 9529.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.119326 restraints weight = 7750.915| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31473 Z= 0.145 Angle : 0.599 16.621 42957 Z= 0.293 Chirality : 0.045 0.344 4920 Planarity : 0.004 0.085 5481 Dihedral : 7.834 112.572 5064 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 12.28 % Favored : 86.21 % 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 (0.13), residues: 3825 helix: 1.23 (0.19), residues: 690 sheet: 0.59 (0.17), residues: 986 loop : -0.20 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.033 0.001 TYR A 873 PHE 0.029 0.002 PHE C 275 TRP 0.017 0.001 TRP A 886 HIS 0.014 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00330 (31389) covalent geometry : angle 0.58125 (42747) SS BOND : bond 0.00864 ( 42) SS BOND : angle 0.98926 ( 84) hydrogen bonds : bond 0.03946 ( 1154) hydrogen bonds : angle 5.93334 ( 3111) link_NAG-ASN : bond 0.00516 ( 42) link_NAG-ASN : angle 2.61878 ( 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 353 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7719 (mp10) REVERT: A 318 PHE cc_start: 0.8599 (t80) cc_final: 0.8240 (t80) REVERT: A 610 VAL cc_start: 0.9005 (t) cc_final: 0.8704 (p) REVERT: A 756 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7635 (t80) REVERT: B 168 PHE cc_start: 0.7970 (t80) cc_final: 0.7718 (t80) REVERT: B 214 ARG cc_start: 0.8458 (mpp-170) cc_final: 0.7033 (tmt170) REVERT: B 265 TYR cc_start: 0.5801 (p90) cc_final: 0.5489 (p90) REVERT: B 707 TYR cc_start: 0.8314 (t80) cc_final: 0.7242 (t80) REVERT: B 730 SER cc_start: 0.8571 (t) cc_final: 0.8230 (p) REVERT: B 741 TYR cc_start: 0.8047 (t80) cc_final: 0.7800 (t80) REVERT: B 901 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: B 906 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: B 1082 CYS cc_start: 0.6349 (t) cc_final: 0.5954 (t) REVERT: B 1139 ASP cc_start: 0.8189 (m-30) cc_final: 0.7972 (t0) REVERT: C 584 ILE cc_start: 0.8106 (mm) cc_final: 0.7575 (mm) REVERT: C 661 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 675 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 731 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7299 (ptp) REVERT: L 37 SER cc_start: 0.3893 (m) cc_final: 0.3666 (t) REVERT: P 115 MET cc_start: 0.4891 (tpp) cc_final: 0.4516 (tpp) outliers start: 50 outliers final: 34 residues processed: 336 average time/residue: 0.1591 time to fit residues: 92.1255 Evaluate side-chains 319 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 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 641 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU 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 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 649 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 912 THR 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: 50.0000 chunk 182 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 153 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.204945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110945 restraints weight = 51807.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115103 restraints weight = 22103.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117698 restraints weight = 13090.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119412 restraints weight = 9316.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120499 restraints weight = 7491.020| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31473 Z= 0.150 Angle : 0.597 16.684 42957 Z= 0.293 Chirality : 0.045 0.357 4920 Planarity : 0.004 0.079 5481 Dihedral : 7.268 104.693 5064 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.21 % Allowed : 13.07 % Favored : 84.72 % 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: 0.33 (0.13), residues: 3825 helix: 1.24 (0.19), residues: 687 sheet: 0.58 (0.17), residues: 968 loop : -0.23 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.028 0.001 TYR A 873 PHE 0.028 0.002 PHE C 275 TRP 0.017 0.001 TRP A 886 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00348 (31389) covalent geometry : angle 0.57864 (42747) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.19100 ( 84) hydrogen bonds : bond 0.03877 ( 1154) hydrogen bonds : angle 5.77418 ( 3111) link_NAG-ASN : bond 0.00517 ( 42) link_NAG-ASN : angle 2.66701 ( 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: 73 poor density : 300 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.6958 (t80) cc_final: 0.6740 (t80) REVERT: A 271 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7823 (mp10) REVERT: A 284 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 318 PHE cc_start: 0.8515 (t80) cc_final: 0.8162 (t80) REVERT: A 610 VAL cc_start: 0.8986 (t) cc_final: 0.8673 (p) REVERT: A 699 LEU cc_start: 0.7982 (tt) cc_final: 0.7480 (tt) REVERT: A 756 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.7651 (t80) REVERT: A 973 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9347 (mt) REVERT: B 168 PHE cc_start: 0.8018 (t80) cc_final: 0.7771 (t80) REVERT: B 177 MET cc_start: 0.8516 (ppp) cc_final: 0.8285 (ppp) REVERT: B 201 PHE cc_start: 0.6710 (t80) cc_final: 0.6459 (t80) REVERT: B 228 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7046 (t70) REVERT: B 265 TYR cc_start: 0.5632 (p90) cc_final: 0.5402 (p90) REVERT: B 707 TYR cc_start: 0.8358 (t80) cc_final: 0.7240 (t80) REVERT: B 730 SER cc_start: 0.8579 (t) cc_final: 0.8257 (p) REVERT: B 741 TYR cc_start: 0.7991 (t80) cc_final: 0.7780 (t80) REVERT: B 873 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7232 (t80) REVERT: B 895 GLN cc_start: 0.7254 (pp30) cc_final: 0.6758 (pp30) REVERT: B 901 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: B 906 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: B 1082 CYS cc_start: 0.6361 (t) cc_final: 0.5973 (t) REVERT: B 1139 ASP cc_start: 0.8142 (m-30) cc_final: 0.7938 (t0) REVERT: C 38 TYR cc_start: 0.8002 (m-80) cc_final: 0.7602 (m-10) REVERT: C 196 ASN cc_start: 0.7614 (p0) cc_final: 0.6558 (t0) REVERT: C 584 ILE cc_start: 0.8074 (mm) cc_final: 0.7529 (mm) REVERT: C 661 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7798 (tm-30) REVERT: C 675 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 731 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7367 (ptp) REVERT: C 1033 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8199 (p) REVERT: L 37 SER cc_start: 0.4012 (m) cc_final: 0.3765 (t) REVERT: P 115 MET cc_start: 0.5193 (tpp) cc_final: 0.4748 (tpp) outliers start: 73 outliers final: 48 residues processed: 350 average time/residue: 0.1604 time to fit residues: 96.0633 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 : 0.896 ------------------------------------------------------------------------------- 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 284 THR 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 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 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 1060 VAL Chi-restraints excluded: chain A residue 1094 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 228 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 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 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 864 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 101 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 371 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 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 = 0.4535 r_free = 0.4535 target = 0.203433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112280 restraints weight = 52447.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116513 restraints weight = 22158.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119246 restraints weight = 12943.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120986 restraints weight = 9097.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122068 restraints weight = 7240.338| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2043 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= 0.113 Angle : 0.579 15.962 42957 Z= 0.281 Chirality : 0.045 0.368 4920 Planarity : 0.004 0.073 5481 Dihedral : 6.931 101.785 5064 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.03 % Allowed : 14.22 % Favored : 83.76 % 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: 1.28 (0.19), residues: 694 sheet: 0.56 (0.17), residues: 988 loop : -0.20 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.022 0.001 TYR A 873 PHE 0.022 0.001 PHE C 275 TRP 0.015 0.001 TRP A 886 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00259 (31389) covalent geometry : angle 0.55936 (42747) SS BOND : bond 0.00275 ( 42) SS BOND : angle 1.16716 ( 84) hydrogen bonds : bond 0.03632 ( 1154) hydrogen bonds : angle 5.54210 ( 3111) link_NAG-ASN : bond 0.00535 ( 42) link_NAG-ASN : angle 2.65871 ( 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 370 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7229 (m90) REVERT: A 271 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7792 (mp10) REVERT: A 318 PHE cc_start: 0.8532 (t80) cc_final: 0.8185 (t80) REVERT: A 610 VAL cc_start: 0.8967 (t) cc_final: 0.8649 (p) REVERT: A 699 LEU cc_start: 0.7942 (tt) cc_final: 0.7564 (tt) REVERT: A 756 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7695 (t80) REVERT: A 895 GLN cc_start: 0.7716 (pp30) cc_final: 0.7302 (pp30) REVERT: B 168 PHE cc_start: 0.8059 (t80) cc_final: 0.7805 (t80) REVERT: B 177 MET cc_start: 0.8516 (ppp) cc_final: 0.8260 (ppp) REVERT: B 214 ARG cc_start: 0.8477 (mpp-170) cc_final: 0.7074 (tmt170) REVERT: B 228 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7330 (t70) REVERT: B 265 TYR cc_start: 0.5669 (p90) cc_final: 0.5389 (p90) REVERT: B 276 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8071 (mm) REVERT: B 587 ILE cc_start: 0.7847 (mt) cc_final: 0.7582 (mp) REVERT: B 707 TYR cc_start: 0.8239 (t80) cc_final: 0.7133 (t80) REVERT: B 777 ASN cc_start: 0.8204 (m-40) cc_final: 0.7873 (m110) REVERT: B 873 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7257 (t80) REVERT: B 895 GLN cc_start: 0.7195 (pp30) cc_final: 0.6601 (pp30) REVERT: B 901 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: B 906 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: B 1082 CYS cc_start: 0.6360 (t) cc_final: 0.5969 (t) REVERT: B 1139 ASP cc_start: 0.8129 (m-30) cc_final: 0.7922 (t0) REVERT: C 38 TYR cc_start: 0.7943 (m-80) cc_final: 0.7507 (m-80) REVERT: C 177 MET cc_start: 0.7018 (mtt) cc_final: 0.6636 (tpt) REVERT: C 196 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6618 (t0) REVERT: C 533 LEU cc_start: 0.8118 (mt) cc_final: 0.7907 (mt) REVERT: C 584 ILE cc_start: 0.8058 (mm) cc_final: 0.7533 (mm) REVERT: C 661 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 675 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 697 MET cc_start: 0.7643 (ptm) cc_final: 0.7426 (ptm) REVERT: C 731 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7312 (ptp) REVERT: C 1107 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7269 (ttm170) REVERT: L 37 SER cc_start: 0.4105 (m) cc_final: 0.3843 (t) REVERT: P 115 MET cc_start: 0.5226 (tpp) cc_final: 0.4764 (tpp) outliers start: 67 outliers final: 45 residues processed: 348 average time/residue: 0.1637 time to fit residues: 97.8127 Evaluate side-chains 337 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 LEU 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 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 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 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 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 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU 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: 5.9990 chunk 182 optimal weight: 0.1980 chunk 205 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 343 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 50.0000 chunk 100 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 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 755 GLN C 895 GLN ** 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 = 0.4527 r_free = 0.4527 target = 0.203317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110256 restraints weight = 51867.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114352 restraints weight = 22292.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116933 restraints weight = 13146.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118642 restraints weight = 9316.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 76)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119713 restraints weight = 7465.447| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31473 Z= 0.150 Angle : 0.599 16.365 42957 Z= 0.292 Chirality : 0.045 0.378 4920 Planarity : 0.004 0.073 5481 Dihedral : 6.825 100.683 5064 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.45 % Allowed : 14.40 % Favored : 83.15 % 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: 0.34 (0.14), residues: 3825 helix: 1.24 (0.19), residues: 688 sheet: 0.53 (0.17), residues: 998 loop : -0.20 (0.14), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.020 0.001 TYR A 873 PHE 0.032 0.002 PHE C 275 TRP 0.019 0.001 TRP A 886 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (31389) covalent geometry : angle 0.57856 (42747) SS BOND : bond 0.00256 ( 42) SS BOND : angle 1.38710 ( 84) hydrogen bonds : bond 0.03709 ( 1154) hydrogen bonds : angle 5.52966 ( 3111) link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 2.70347 ( 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 370 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 289 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7822 (mp10) REVERT: A 306 PHE cc_start: 0.6865 (m-80) cc_final: 0.6527 (m-80) REVERT: A 610 VAL cc_start: 0.8971 (t) cc_final: 0.8661 (p) REVERT: A 699 LEU cc_start: 0.8002 (tt) cc_final: 0.7540 (tt) REVERT: A 756 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7721 (t80) REVERT: A 895 GLN cc_start: 0.7757 (pp30) cc_final: 0.7310 (pp30) REVERT: B 168 PHE cc_start: 0.8107 (t80) cc_final: 0.7900 (t80) REVERT: B 177 MET cc_start: 0.8552 (ppp) cc_final: 0.8307 (ppp) REVERT: B 214 ARG cc_start: 0.8472 (mpp-170) cc_final: 0.7168 (tmt170) REVERT: B 228 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7505 (t70) REVERT: B 265 TYR cc_start: 0.5657 (p90) cc_final: 0.5383 (p90) REVERT: B 276 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7956 (mm) REVERT: B 707 TYR cc_start: 0.8365 (t80) cc_final: 0.7244 (t80) REVERT: B 777 ASN cc_start: 0.8263 (m-40) cc_final: 0.7854 (m110) REVERT: B 873 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 895 GLN cc_start: 0.7225 (pp30) cc_final: 0.6578 (pp30) REVERT: B 901 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: B 906 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: B 943 SER cc_start: 0.8368 (m) cc_final: 0.8059 (p) REVERT: B 1082 CYS cc_start: 0.6370 (t) cc_final: 0.5974 (t) REVERT: B 1139 ASP cc_start: 0.8127 (m-30) cc_final: 0.7922 (t0) REVERT: C 38 TYR cc_start: 0.8059 (m-80) cc_final: 0.7646 (m-10) REVERT: C 584 ILE cc_start: 0.8076 (mm) cc_final: 0.7537 (mm) REVERT: C 661 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 731 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7355 (ptp) REVERT: C 823 PHE cc_start: 0.8069 (t80) cc_final: 0.7723 (t80) REVERT: C 895 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6726 (pp30) REVERT: C 1028 LYS cc_start: 0.7217 (mmtm) cc_final: 0.6962 (tppt) REVERT: C 1107 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7274 (ttm170) REVERT: H 21 MET cc_start: 0.1275 (ptt) cc_final: 0.1066 (ptt) REVERT: L 37 SER cc_start: 0.4050 (m) cc_final: 0.3789 (t) REVERT: P 115 MET cc_start: 0.5295 (tpp) cc_final: 0.4785 (tpp) outliers start: 81 outliers final: 56 residues processed: 347 average time/residue: 0.1573 time to fit residues: 93.9882 Evaluate side-chains 337 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 273 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 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 228 ASP Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 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 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 895 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 1066 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 151 optimal weight: 6.9990 chunk 222 optimal weight: 50.0000 chunk 138 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 371 optimal weight: 50.0000 chunk 120 optimal weight: 9.9990 chunk 363 optimal weight: 50.0000 chunk 282 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 290 optimal weight: 0.0870 chunk 248 optimal weight: 7.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1036 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.200115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105203 restraints weight = 52902.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108998 restraints weight = 23459.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.111438 restraints weight = 14249.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112956 restraints weight = 10314.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113974 restraints weight = 8406.587| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31473 Z= 0.247 Angle : 0.692 18.430 42957 Z= 0.343 Chirality : 0.047 0.405 4920 Planarity : 0.005 0.090 5481 Dihedral : 7.061 100.846 5064 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.87 % Allowed : 14.58 % Favored : 82.55 % 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: 0.17 (0.14), residues: 3825 helix: 0.88 (0.19), residues: 682 sheet: 0.58 (0.17), residues: 987 loop : -0.31 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.021 0.002 TYR B1067 PHE 0.035 0.002 PHE C 275 TRP 0.022 0.001 TRP A 886 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00571 (31389) covalent geometry : angle 0.67147 (42747) SS BOND : bond 0.00416 ( 42) SS BOND : angle 1.58360 ( 84) hydrogen bonds : bond 0.04252 ( 1154) hydrogen bonds : angle 5.82928 ( 3111) link_NAG-ASN : bond 0.00568 ( 42) link_NAG-ASN : angle 2.91325 ( 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 366 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 271 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8249 (mp10) REVERT: A 284 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (t) REVERT: A 610 VAL cc_start: 0.9122 (t) cc_final: 0.8816 (p) REVERT: B 168 PHE cc_start: 0.8125 (t80) cc_final: 0.7919 (t80) REVERT: B 177 MET cc_start: 0.8618 (ppp) cc_final: 0.8369 (ppp) REVERT: B 214 ARG cc_start: 0.8517 (mpp-170) cc_final: 0.7243 (tmt170) REVERT: B 228 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7519 (t70) REVERT: B 276 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 707 TYR cc_start: 0.8422 (t80) cc_final: 0.7220 (t80) REVERT: B 873 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7398 (t80) REVERT: B 895 GLN cc_start: 0.7441 (pp30) cc_final: 0.6854 (pp30) REVERT: B 901 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: B 906 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: B 943 SER cc_start: 0.8418 (m) cc_final: 0.8117 (p) REVERT: B 1082 CYS cc_start: 0.6506 (t) cc_final: 0.6117 (t) REVERT: C 38 TYR cc_start: 0.8184 (m-80) cc_final: 0.7782 (m-10) REVERT: C 584 ILE cc_start: 0.8163 (mm) cc_final: 0.7652 (mm) REVERT: C 731 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7266 (ptp) REVERT: C 823 PHE cc_start: 0.8233 (t80) cc_final: 0.7854 (t80) REVERT: C 872 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: C 1107 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: H 21 MET cc_start: 0.2028 (ptt) cc_final: 0.1817 (ptt) REVERT: L 37 SER cc_start: 0.3955 (m) cc_final: 0.3711 (t) REVERT: P 115 MET cc_start: 0.5451 (tpp) cc_final: 0.4946 (tpp) outliers start: 95 outliers final: 72 residues processed: 340 average time/residue: 0.1535 time to fit residues: 90.7478 Evaluate side-chains 336 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 255 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR 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 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL 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 1012 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 LEU 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 770 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 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 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 951 VAL 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 C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 311 optimal weight: 0.3980 chunk 182 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 293 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 221 optimal weight: 0.3980 chunk 340 optimal weight: 50.0000 chunk 236 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** 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** L 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.204856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112286 restraints weight = 51881.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117359 restraints weight = 23026.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119124 restraints weight = 12339.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120350 restraints weight = 8616.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120577 restraints weight = 8065.088| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 31473 Z= 0.114 Angle : 0.610 18.367 42957 Z= 0.293 Chirality : 0.045 0.386 4920 Planarity : 0.004 0.087 5481 Dihedral : 6.632 98.043 5064 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.91 % Allowed : 15.67 % Favored : 82.43 % 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: 0.28 (0.14), residues: 3825 helix: 1.18 (0.19), residues: 683 sheet: 0.55 (0.17), residues: 975 loop : -0.26 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.023 0.001 TYR A 170 PHE 0.051 0.002 PHE C 55 TRP 0.013 0.001 TRP A 886 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00257 (31389) covalent geometry : angle 0.59025 (42747) SS BOND : bond 0.00200 ( 42) SS BOND : angle 1.33031 ( 84) hydrogen bonds : bond 0.03572 ( 1154) hydrogen bonds : angle 5.39696 ( 3111) link_NAG-ASN : bond 0.00534 ( 42) link_NAG-ASN : angle 2.74170 ( 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 361 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 298 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7878 (mp10) REVERT: A 284 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8467 (t) REVERT: A 610 VAL cc_start: 0.8940 (t) cc_final: 0.8632 (p) REVERT: A 756 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7770 (t80) REVERT: A 895 GLN cc_start: 0.8278 (pm20) cc_final: 0.7621 (pp30) REVERT: B 168 PHE cc_start: 0.7990 (t80) cc_final: 0.7742 (t80) REVERT: B 177 MET cc_start: 0.8634 (ppp) cc_final: 0.8385 (ppp) REVERT: B 214 ARG cc_start: 0.8546 (mpp-170) cc_final: 0.7292 (tmt170) REVERT: B 265 TYR cc_start: 0.5275 (p90) cc_final: 0.5011 (p90) REVERT: B 276 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 587 ILE cc_start: 0.7883 (mt) cc_final: 0.7632 (mp) REVERT: B 697 MET cc_start: 0.8719 (tpp) cc_final: 0.8461 (mmt) REVERT: B 707 TYR cc_start: 0.8257 (t80) cc_final: 0.7127 (t80) REVERT: B 731 MET cc_start: 0.8091 (ptp) cc_final: 0.7624 (ptp) REVERT: B 777 ASN cc_start: 0.8144 (m-40) cc_final: 0.7944 (m110) REVERT: B 873 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7156 (t80) REVERT: B 895 GLN cc_start: 0.7310 (pp30) cc_final: 0.6600 (pp30) REVERT: B 901 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: B 902 MET cc_start: 0.7862 (tpp) cc_final: 0.7571 (tpp) REVERT: B 906 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: B 943 SER cc_start: 0.8450 (m) cc_final: 0.8155 (p) REVERT: B 1082 CYS cc_start: 0.6329 (t) cc_final: 0.5910 (t) REVERT: C 38 TYR cc_start: 0.8019 (m-80) cc_final: 0.7505 (m-80) REVERT: C 529 LYS cc_start: 0.8248 (mtpp) cc_final: 0.8020 (mmmt) REVERT: C 584 ILE cc_start: 0.8145 (mm) cc_final: 0.7641 (mm) REVERT: C 661 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 731 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7310 (ptp) REVERT: C 1092 GLU cc_start: 0.8619 (tp30) cc_final: 0.8401 (tp30) REVERT: C 1107 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: L 37 SER cc_start: 0.4135 (m) cc_final: 0.3861 (t) REVERT: P 115 MET cc_start: 0.5310 (tpp) cc_final: 0.4818 (tpp) outliers start: 63 outliers final: 46 residues processed: 343 average time/residue: 0.1629 time to fit residues: 95.5723 Evaluate side-chains 331 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 284 THR 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 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 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 159 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 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 904 TYR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 34 optimal weight: 8.9990 chunk 146 optimal weight: 50.0000 chunk 292 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 82 optimal weight: 0.0050 chunk 191 optimal weight: 2.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B1054 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.209323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115612 restraints weight = 50728.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120689 restraints weight = 22853.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122517 restraints weight = 12638.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123563 restraints weight = 8737.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123896 restraints weight = 8106.910| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31473 Z= 0.144 Angle : 0.618 18.567 42957 Z= 0.299 Chirality : 0.045 0.394 4920 Planarity : 0.005 0.078 5481 Dihedral : 6.596 97.738 5064 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 16.30 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3825 helix: 1.16 (0.19), residues: 677 sheet: 0.59 (0.16), residues: 1014 loop : -0.26 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.023 0.001 TYR B 873 PHE 0.059 0.002 PHE C 55 TRP 0.017 0.001 TRP A 886 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00337 (31389) covalent geometry : angle 0.59880 (42747) SS BOND : bond 0.00244 ( 42) SS BOND : angle 1.33742 ( 84) hydrogen bonds : bond 0.03637 ( 1154) hydrogen bonds : angle 5.40428 ( 3111) link_NAG-ASN : bond 0.00508 ( 42) link_NAG-ASN : angle 2.74458 ( 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 338 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8020 (mp10) REVERT: A 284 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8437 (t) REVERT: A 584 ILE cc_start: 0.8632 (mm) cc_final: 0.8424 (mm) REVERT: A 610 VAL cc_start: 0.9021 (t) cc_final: 0.8719 (p) REVERT: A 756 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 895 GLN cc_start: 0.8297 (pm20) cc_final: 0.7667 (pp30) REVERT: B 177 MET cc_start: 0.8687 (ppp) cc_final: 0.8408 (ppp) REVERT: B 214 ARG cc_start: 0.8564 (mpp-170) cc_final: 0.7251 (tmt170) REVERT: B 265 TYR cc_start: 0.5267 (p90) cc_final: 0.5033 (p90) REVERT: B 276 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8006 (mm) REVERT: B 697 MET cc_start: 0.8873 (tpp) cc_final: 0.8584 (mmt) REVERT: B 707 TYR cc_start: 0.8371 (t80) cc_final: 0.7184 (t80) REVERT: B 777 ASN cc_start: 0.8252 (m-40) cc_final: 0.7838 (m110) REVERT: B 873 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 895 GLN cc_start: 0.7300 (pp30) cc_final: 0.6572 (pp30) REVERT: B 901 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: B 906 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: B 943 SER cc_start: 0.8435 (m) cc_final: 0.8141 (p) REVERT: B 1082 CYS cc_start: 0.6489 (t) cc_final: 0.6105 (t) REVERT: C 38 TYR cc_start: 0.8081 (m-80) cc_final: 0.7614 (m-80) REVERT: C 110 LEU cc_start: 0.8812 (tp) cc_final: 0.8441 (mp) REVERT: C 529 LYS cc_start: 0.8298 (mtpp) cc_final: 0.8066 (mmmt) REVERT: C 584 ILE cc_start: 0.8162 (mm) cc_final: 0.7661 (mm) REVERT: C 731 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7354 (ptp) REVERT: C 823 PHE cc_start: 0.8066 (t80) cc_final: 0.7662 (t80) REVERT: C 895 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7227 (pp30) REVERT: C 1107 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7268 (ttm170) REVERT: L 37 SER cc_start: 0.4151 (m) cc_final: 0.3889 (t) REVERT: P 115 MET cc_start: 0.5285 (tpp) cc_final: 0.4723 (tpp) outliers start: 61 outliers final: 49 residues processed: 323 average time/residue: 0.1571 time to fit residues: 87.5263 Evaluate side-chains 320 residues out of total 3366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 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 911 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 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 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 98 optimal weight: 0.9980 chunk 302 optimal weight: 0.5980 chunk 309 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 205 optimal weight: 0.4980 chunk 364 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.204706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111074 restraints weight = 52313.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115351 restraints weight = 24154.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116809 restraints weight = 14289.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118657 restraints weight = 9291.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118734 restraints weight = 7739.566| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31473 Z= 0.145 Angle : 0.722 59.200 42957 Z= 0.377 Chirality : 0.046 0.685 4920 Planarity : 0.005 0.095 5481 Dihedral : 6.596 97.762 5064 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.78 % Allowed : 16.55 % Favored : 81.67 % Cbeta Deviations : 0.03 % 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: 0.30 (0.14), residues: 3825 helix: 1.16 (0.19), residues: 677 sheet: 0.59 (0.16), residues: 1014 loop : -0.26 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.074 0.001 TYR H 112A PHE 0.049 0.002 PHE C 55 TRP 0.016 0.001 TRP A 886 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00329 (31389) covalent geometry : angle 0.70636 (42747) SS BOND : bond 0.00249 ( 42) SS BOND : angle 1.31977 ( 84) hydrogen bonds : bond 0.03624 ( 1154) hydrogen bonds : angle 5.40210 ( 3111) link_NAG-ASN : bond 0.00506 ( 42) link_NAG-ASN : angle 2.73851 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8563.89 seconds wall clock time: 146 minutes 55.47 seconds (8815.47 seconds total)