Starting phenix.real_space_refine on Sat Mar 7 00:50:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cwn_30484/03_2026/7cwn_30484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwn_30484/03_2026/7cwn_30484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cwn_30484/03_2026/7cwn_30484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwn_30484/03_2026/7cwn_30484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cwn_30484/03_2026/7cwn_30484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwn_30484/03_2026/7cwn_30484.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 153 5.16 5 C 22984 2.51 5 N 5990 2.21 5 O 7064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 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: 36191 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8348 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 8339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8339 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 50, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 8351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8351 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 1020} Chain breaks: 6 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.63, per 1000 atoms: 0.21 Number of scatterers: 36191 At special positions: 0 Unit cell: (186.16, 188.24, 204.88, 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 153 16.00 O 7064 8.00 N 5990 7.00 C 22984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.09 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=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.04 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=2.02 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=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.00 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.01 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 87 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 87 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN A1098 " " NAG T 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8534 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 79 sheets defined 17.9% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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 1140 through 1146 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.749A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.506A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.500A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 4.023A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.544A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.598A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (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 1140 through 1146 removed outlier: 4.038A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.981A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.634A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.707A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.882A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.517A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) 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 982 removed outlier: 3.539A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.617A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.450A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.843A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.661A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.094A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.193A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.014A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.841A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.847A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.275A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.805A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.010A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.839A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.349A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.549A pdb=" N THR K 113 " --> pdb=" O TYR K 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 4 through 7 removed outlier: 11.871A pdb=" N CYS I 23 " --> pdb=" O THR I 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR I 74 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA I 25 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR I 72 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN I 27 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP I 70 " --> pdb=" O GLN I 27 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AG4, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.338A pdb=" N GLN D 10 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.086A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR L 113 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET L 34 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 4 through 7 removed outlier: 11.869A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN J 27 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AH4, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.337A pdb=" N GLN N 10 " --> pdb=" O GLU N 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'N' and resid 52 through 53 removed outlier: 6.085A pdb=" N TRP N 34 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AH7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AH9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR G 113 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS F 23 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR F 74 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA F 25 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR F 72 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN F 27 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP F 70 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AI4, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.339A pdb=" N GLN M 10 " --> pdb=" O GLU M 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'M' and resid 52 through 53 removed outlier: 6.085A pdb=" N TRP M 34 " --> pdb=" O LEU M 46 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AI7, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3165 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: 9.47 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8436 1.33 - 1.45: 9503 1.45 - 1.58: 18868 1.58 - 1.70: 0 1.70 - 1.83: 195 Bond restraints: 37002 Sorted by residual: bond pdb=" N THR C 588 " pdb=" CA THR C 588 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.80e-03 1.04e+04 1.50e+01 bond pdb=" CA SER C 60 " pdb=" CB SER C 60 " ideal model delta sigma weight residual 1.533 1.476 0.057 1.51e-02 4.39e+03 1.43e+01 bond pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 1.455 1.491 -0.036 9.60e-03 1.09e+04 1.42e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 36997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 48561 2.75 - 5.51: 1610 5.51 - 8.26: 109 8.26 - 11.01: 24 11.01 - 13.76: 9 Bond angle restraints: 50313 Sorted by residual: angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 100 " ideal model delta sigma weight residual 113.20 102.81 10.39 9.60e-01 1.09e+00 1.17e+02 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.20 102.85 10.35 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N CYS A 301 " pdb=" CA CYS A 301 " pdb=" C CYS A 301 " ideal model delta sigma weight residual 113.23 102.41 10.82 1.24e+00 6.50e-01 7.61e+01 angle pdb=" C TRP M 93 " pdb=" CA TRP M 93 " pdb=" CB TRP M 93 " ideal model delta sigma weight residual 110.17 123.93 -13.76 1.97e+00 2.58e-01 4.88e+01 angle pdb=" C TRP N 93 " pdb=" CA TRP N 93 " pdb=" CB TRP N 93 " ideal model delta sigma weight residual 110.17 123.93 -13.76 1.97e+00 2.58e-01 4.88e+01 ... (remaining 50308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 21447 16.86 - 33.72: 877 33.72 - 50.58: 193 50.58 - 67.43: 44 67.43 - 84.29: 15 Dihedral angle restraints: 22576 sinusoidal: 9268 harmonic: 13308 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.00 73.00 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.91 72.91 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.30 72.30 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 22573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 5787 0.314 - 0.628: 17 0.628 - 0.942: 0 0.942 - 1.257: 0 1.257 - 1.571: 2 Chirality restraints: 5806 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.17e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-01 2.50e+01 4.87e+01 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 ... (remaining 5803 not shown) Planarity restraints: 6443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.332 2.00e-02 2.50e+03 2.81e-01 9.86e+02 pdb=" C7 NAG Y 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.262 2.00e-02 2.50e+03 2.24e-01 6.25e+02 pdb=" C7 NAG d 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN C 234 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG Z 1 " -0.121 2.00e-02 2.50e+03 ... (remaining 6440 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 26 2.13 - 2.82: 11470 2.82 - 3.51: 50102 3.51 - 4.21: 86679 4.21 - 4.90: 147248 Nonbonded interactions: 295525 Sorted by model distance: nonbonded pdb=" O TYR B 369 " pdb=" NE1 TRP D 93 " model vdw 1.435 3.120 nonbonded pdb=" O TYR A 369 " pdb=" NE1 TRP M 93 " model vdw 1.436 3.120 nonbonded pdb=" O TYR C 369 " pdb=" NE1 TRP N 93 " model vdw 1.436 3.120 nonbonded pdb=" CD2 LEU B 48 " pdb=" CE2 PHE B 306 " model vdw 1.462 3.760 nonbonded pdb=" O ALA C 372 " pdb=" O PHE N 92 " model vdw 1.544 3.040 ... (remaining 295520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 330 or resid 335 through 526 or resid 531 throu \ gh 698 or (resid 699 and (name N or name CA or name C or name O or name CB )) or \ resid 700 through 1305)) selection = (chain 'B' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 698 or (resid 699 and (name N or n \ ame CA or name C or name O or name CB )) or resid 700 through 1305)) selection = (chain 'C' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 330 or resid 335 through 526 or re \ sid 531 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'E' and (resid 2 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 123)) selection = chain 'H' selection = (chain 'O' and (resid 2 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 123)) } ncs_group { reference = chain 'F' selection = (chain 'I' and resid 1 through 107) selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 34.570 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 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 : 0.009 0.393 37098 Z= 0.483 Angle : 1.137 25.667 50550 Z= 0.686 Chirality : 0.073 1.571 5806 Planarity : 0.008 0.281 6413 Dihedral : 10.187 84.293 13889 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 0.18 % Allowed : 2.16 % Favored : 97.66 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.49 (0.10), residues: 4517 helix: -3.30 (0.15), residues: 580 sheet: -1.89 (0.14), residues: 1029 loop : -2.37 (0.09), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 61 TYR 0.034 0.003 TYR E 50 PHE 0.035 0.003 PHE C 392 TRP 0.027 0.004 TRP N 93 HIS 0.012 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00835 (37002) covalent geometry : angle 1.11439 (50313) SS BOND : bond 0.01371 ( 51) SS BOND : angle 1.52779 ( 102) hydrogen bonds : bond 0.26619 ( 1200) hydrogen bonds : angle 11.38961 ( 3165) link_BETA1-4 : bond 0.00743 ( 15) link_BETA1-4 : angle 3.22245 ( 45) link_NAG-ASN : bond 0.10133 ( 30) link_NAG-ASN : angle 4.93546 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 331 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.6851 (p) cc_final: 0.6538 (p) REVERT: A 124 THR cc_start: 0.6683 (t) cc_final: 0.6433 (m) REVERT: B 51 THR cc_start: 0.6956 (p) cc_final: 0.6665 (p) REVERT: B 52 GLN cc_start: 0.7568 (pt0) cc_final: 0.7123 (tp40) REVERT: C 51 THR cc_start: 0.6856 (p) cc_final: 0.6612 (p) REVERT: C 52 GLN cc_start: 0.7488 (pt0) cc_final: 0.6917 (tp40) REVERT: C 287 ASP cc_start: 0.6181 (t0) cc_final: 0.5927 (m-30) outliers start: 7 outliers final: 1 residues processed: 337 average time/residue: 0.2214 time to fit residues: 122.0100 Evaluate side-chains 135 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 122 ASN A 321 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 655 HIS A 658 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 134 GLN B 321 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 655 HIS B 658 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 148 ASN C 282 ASN C 317 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 655 HIS C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 935 GLN C1010 GLN K 84 ASN K 104 ASN I 38 GLN I 55 GLN ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN L 84 ASN L 104 ASN J 38 GLN J 55 GLN ** N 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN G 84 ASN G 104 ASN F 38 GLN F 55 GLN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.129787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.095052 restraints weight = 145813.709| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 5.48 r_work: 0.3584 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37098 Z= 0.183 Angle : 0.743 15.845 50550 Z= 0.384 Chirality : 0.049 0.705 5806 Planarity : 0.005 0.059 6413 Dihedral : 7.684 59.287 5893 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 1.32 % Allowed : 5.13 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.40 (0.11), residues: 4517 helix: -0.96 (0.19), residues: 621 sheet: -1.30 (0.14), residues: 1242 loop : -1.94 (0.11), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 98 TYR 0.026 0.002 TYR H 50 PHE 0.042 0.002 PHE B 106 TRP 0.021 0.002 TRP I 35 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00393 (37002) covalent geometry : angle 0.72475 (50313) SS BOND : bond 0.00397 ( 51) SS BOND : angle 1.68206 ( 102) hydrogen bonds : bond 0.05043 ( 1200) hydrogen bonds : angle 7.51551 ( 3165) link_BETA1-4 : bond 0.00704 ( 15) link_BETA1-4 : angle 2.38736 ( 45) link_NAG-ASN : bond 0.00489 ( 30) link_NAG-ASN : angle 3.24502 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 VAL cc_start: 0.8281 (t) cc_final: 0.8026 (m) REVERT: A 564 GLN cc_start: 0.8092 (tp40) cc_final: 0.7649 (tp40) REVERT: B 59 PHE cc_start: 0.8058 (m-10) cc_final: 0.7728 (m-10) REVERT: B 128 ILE cc_start: 0.7332 (mt) cc_final: 0.7117 (mp) REVERT: B 239 GLN cc_start: 0.7589 (tt0) cc_final: 0.6957 (tp40) REVERT: B 564 GLN cc_start: 0.8031 (tp40) cc_final: 0.7417 (tp40) REVERT: B 740 MET cc_start: 0.8371 (ttt) cc_final: 0.8150 (ttp) REVERT: C 772 VAL cc_start: 0.9287 (p) cc_final: 0.9059 (m) REVERT: D 23 ARG cc_start: 0.4458 (mtt180) cc_final: 0.4029 (ttp80) REVERT: D 96 ILE cc_start: 0.5341 (OUTLIER) cc_final: 0.4774 (tp) REVERT: N 96 ILE cc_start: 0.5109 (OUTLIER) cc_final: 0.4614 (tp) REVERT: H 96 CYS cc_start: -0.1174 (p) cc_final: -0.1478 (p) REVERT: G 96 CYS cc_start: 0.2467 (OUTLIER) cc_final: 0.1952 (t) REVERT: M 23 ARG cc_start: 0.5087 (mtt180) cc_final: 0.4506 (ttp80) REVERT: M 96 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4826 (tp) REVERT: O 96 CYS cc_start: -0.1195 (p) cc_final: -0.1435 (p) outliers start: 52 outliers final: 22 residues processed: 205 average time/residue: 0.2151 time to fit residues: 75.8393 Evaluate side-chains 145 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 172 optimal weight: 2.9990 chunk 213 optimal weight: 0.1980 chunk 329 optimal weight: 50.0000 chunk 212 optimal weight: 0.9980 chunk 363 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 353 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1010 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 GLN E 6 GLN E 39 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 GLN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN F 38 GLN M 10 GLN O 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.127719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.090863 restraints weight = 144139.235| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 5.68 r_work: 0.3508 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 37098 Z= 0.209 Angle : 0.677 16.747 50550 Z= 0.343 Chirality : 0.047 0.640 5806 Planarity : 0.004 0.054 6413 Dihedral : 6.797 59.017 5893 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 1.93 % Allowed : 6.51 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.92 (0.12), residues: 4517 helix: -0.05 (0.20), residues: 643 sheet: -1.14 (0.14), residues: 1275 loop : -1.68 (0.11), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.043 0.002 TYR I 92 PHE 0.035 0.002 PHE C 855 TRP 0.023 0.002 TRP G 36 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00457 (37002) covalent geometry : angle 0.65815 (50313) SS BOND : bond 0.00379 ( 51) SS BOND : angle 1.02463 ( 102) hydrogen bonds : bond 0.04370 ( 1200) hydrogen bonds : angle 6.58633 ( 3165) link_BETA1-4 : bond 0.00573 ( 15) link_BETA1-4 : angle 2.62518 ( 45) link_NAG-ASN : bond 0.00693 ( 30) link_NAG-ASN : angle 3.20917 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 136 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7041 (t80) cc_final: 0.6816 (t80) REVERT: A 177 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7073 (mpp) REVERT: A 534 VAL cc_start: 0.8491 (t) cc_final: 0.8251 (m) REVERT: A 697 MET cc_start: 0.7922 (ttm) cc_final: 0.7544 (mtp) REVERT: A 869 MET cc_start: 0.8780 (mtt) cc_final: 0.8521 (mmm) REVERT: A 1138 TYR cc_start: 0.8381 (t80) cc_final: 0.7815 (t80) REVERT: B 697 MET cc_start: 0.8062 (ttm) cc_final: 0.7663 (mtp) REVERT: B 1089 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: C 170 TYR cc_start: 0.7267 (t80) cc_final: 0.6684 (t80) REVERT: C 200 TYR cc_start: 0.7434 (m-10) cc_final: 0.7180 (m-10) REVERT: C 868 GLU cc_start: 0.8500 (tt0) cc_final: 0.8258 (tp30) REVERT: C 1029 MET cc_start: 0.9157 (tpp) cc_final: 0.8818 (tpp) REVERT: D 10 GLN cc_start: 0.1125 (OUTLIER) cc_final: -0.0123 (tp40) REVERT: N 10 GLN cc_start: 0.1455 (OUTLIER) cc_final: -0.0673 (tp40) REVERT: N 49 TYR cc_start: 0.5406 (m-10) cc_final: 0.4651 (m-80) REVERT: H 96 CYS cc_start: -0.0357 (p) cc_final: -0.0584 (p) REVERT: M 10 GLN cc_start: 0.2058 (OUTLIER) cc_final: 0.0001 (tp40) REVERT: M 23 ARG cc_start: 0.4995 (mtt180) cc_final: 0.4508 (ttp80) REVERT: M 49 TYR cc_start: 0.5197 (m-80) cc_final: 0.4832 (m-80) REVERT: M 69 ASP cc_start: 0.5632 (t0) cc_final: 0.5219 (t70) outliers start: 76 outliers final: 31 residues processed: 190 average time/residue: 0.1939 time to fit residues: 65.0194 Evaluate side-chains 146 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 10 GLN Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain M residue 10 GLN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 45 optimal weight: 6.9990 chunk 341 optimal weight: 0.0570 chunk 141 optimal weight: 9.9990 chunk 433 optimal weight: 0.5980 chunk 346 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** M 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.128076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.091381 restraints weight = 143206.919| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 5.25 r_work: 0.3555 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37098 Z= 0.146 Angle : 0.616 16.055 50550 Z= 0.309 Chirality : 0.045 0.621 5806 Planarity : 0.004 0.047 6413 Dihedral : 6.272 59.138 5893 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 2.01 % Allowed : 7.12 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.62 (0.12), residues: 4517 helix: 0.37 (0.20), residues: 654 sheet: -0.82 (0.14), residues: 1220 loop : -1.62 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.023 0.001 TYR H 32 PHE 0.017 0.002 PHE B 392 TRP 0.030 0.001 TRP I 35 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 (37002) covalent geometry : angle 0.59538 (50313) SS BOND : bond 0.00290 ( 51) SS BOND : angle 1.72905 ( 102) hydrogen bonds : bond 0.03718 ( 1200) hydrogen bonds : angle 6.11311 ( 3165) link_BETA1-4 : bond 0.00626 ( 15) link_BETA1-4 : angle 2.45097 ( 45) link_NAG-ASN : bond 0.00490 ( 30) link_NAG-ASN : angle 2.89616 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 122 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8436 (mp10) cc_final: 0.7948 (mt0) REVERT: A 170 TYR cc_start: 0.6912 (t80) cc_final: 0.6576 (t80) REVERT: A 177 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7058 (mpp) REVERT: A 534 VAL cc_start: 0.8497 (t) cc_final: 0.8240 (m) REVERT: A 697 MET cc_start: 0.7743 (ttm) cc_final: 0.7355 (mtp) REVERT: A 855 PHE cc_start: 0.7677 (m-10) cc_final: 0.7101 (m-10) REVERT: A 869 MET cc_start: 0.8574 (mtt) cc_final: 0.8361 (mmm) REVERT: A 1138 TYR cc_start: 0.8436 (t80) cc_final: 0.7916 (t80) REVERT: B 1089 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: C 52 GLN cc_start: 0.8481 (mp10) cc_final: 0.7880 (mt0) REVERT: C 200 TYR cc_start: 0.7269 (m-10) cc_final: 0.7052 (m-10) REVERT: C 745 ASP cc_start: 0.7226 (m-30) cc_final: 0.6585 (t0) REVERT: C 1029 MET cc_start: 0.9068 (tpp) cc_final: 0.8792 (tpp) REVERT: C 1145 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7305 (tt) REVERT: K 70 ILE cc_start: 0.0855 (OUTLIER) cc_final: 0.0507 (mp) REVERT: D 10 GLN cc_start: -0.0094 (mt0) cc_final: -0.0667 (tp40) REVERT: D 49 TYR cc_start: 0.5239 (m-80) cc_final: 0.4977 (m-80) REVERT: L 70 ILE cc_start: 0.1349 (OUTLIER) cc_final: 0.0948 (mp) REVERT: N 4 LEU cc_start: 0.2664 (OUTLIER) cc_final: 0.2396 (pp) REVERT: N 10 GLN cc_start: -0.0172 (mt0) cc_final: -0.0938 (tp40) REVERT: N 49 TYR cc_start: 0.5524 (m-10) cc_final: 0.4776 (m-80) REVERT: N 96 ILE cc_start: 0.4922 (OUTLIER) cc_final: 0.4513 (tp) REVERT: H 96 CYS cc_start: -0.0560 (p) cc_final: -0.0820 (p) REVERT: M 4 LEU cc_start: 0.2396 (OUTLIER) cc_final: 0.1884 (pp) REVERT: M 10 GLN cc_start: 0.0652 (mt0) cc_final: -0.0636 (tp40) REVERT: M 49 TYR cc_start: 0.5176 (m-80) cc_final: 0.4914 (m-80) REVERT: M 69 ASP cc_start: 0.5626 (t0) cc_final: 0.5220 (t70) outliers start: 79 outliers final: 39 residues processed: 198 average time/residue: 0.1938 time to fit residues: 68.0755 Evaluate side-chains 151 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 216 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 450 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 399 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 262 optimal weight: 30.0000 chunk 202 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 901 GLN B1142 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 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 = 0.4632 r_free = 0.4632 target = 0.137329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.101946 restraints weight = 134124.539| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 4.49 r_work: 0.3573 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37098 Z= 0.127 Angle : 0.586 15.059 50550 Z= 0.290 Chirality : 0.044 0.577 5806 Planarity : 0.004 0.044 6413 Dihedral : 5.803 59.445 5893 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 1.55 % Allowed : 8.11 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.46 (0.12), residues: 4517 helix: 0.66 (0.20), residues: 653 sheet: -0.85 (0.14), residues: 1276 loop : -1.48 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 23 TYR 0.023 0.001 TYR B 170 PHE 0.021 0.001 PHE C 855 TRP 0.019 0.001 TRP G 36 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00275 (37002) covalent geometry : angle 0.56807 (50313) SS BOND : bond 0.00266 ( 51) SS BOND : angle 1.05429 ( 102) hydrogen bonds : bond 0.03550 ( 1200) hydrogen bonds : angle 5.81393 ( 3165) link_BETA1-4 : bond 0.00554 ( 15) link_BETA1-4 : angle 2.43737 ( 45) link_NAG-ASN : bond 0.00489 ( 30) link_NAG-ASN : angle 2.84472 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 1.384 Fit side-chains REVERT: A 52 GLN cc_start: 0.8309 (mp10) cc_final: 0.7923 (mt0) REVERT: A 170 TYR cc_start: 0.6923 (t80) cc_final: 0.6689 (t80) REVERT: A 177 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6838 (mpp) REVERT: A 534 VAL cc_start: 0.8538 (t) cc_final: 0.8289 (m) REVERT: A 697 MET cc_start: 0.7943 (ttm) cc_final: 0.7440 (mtp) REVERT: A 855 PHE cc_start: 0.7585 (m-10) cc_final: 0.7214 (m-10) REVERT: A 869 MET cc_start: 0.8664 (mtt) cc_final: 0.8402 (mmm) REVERT: A 1135 ASN cc_start: 0.8470 (t0) cc_final: 0.8235 (t0) REVERT: A 1138 TYR cc_start: 0.8498 (t80) cc_final: 0.8029 (t80) REVERT: B 170 TYR cc_start: 0.7217 (t80) cc_final: 0.6971 (t80) REVERT: B 697 MET cc_start: 0.7890 (ttm) cc_final: 0.7567 (mtp) REVERT: B 855 PHE cc_start: 0.7638 (m-10) cc_final: 0.7051 (m-10) REVERT: C 200 TYR cc_start: 0.7417 (m-10) cc_final: 0.7208 (m-10) REVERT: C 745 ASP cc_start: 0.6696 (m-30) cc_final: 0.6437 (t0) REVERT: C 1029 MET cc_start: 0.9110 (tpp) cc_final: 0.8836 (tpp) REVERT: C 1145 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7188 (tt) REVERT: K 70 ILE cc_start: 0.1334 (OUTLIER) cc_final: 0.0860 (mp) REVERT: D 10 GLN cc_start: -0.0086 (mt0) cc_final: -0.0942 (tp40) REVERT: D 49 TYR cc_start: 0.5035 (m-80) cc_final: 0.4641 (m-80) REVERT: E 64 PHE cc_start: 0.4981 (p90) cc_final: 0.4433 (p90) REVERT: N 10 GLN cc_start: -0.0018 (mt0) cc_final: -0.0956 (tp40) REVERT: N 19 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6448 (m) REVERT: N 96 ILE cc_start: 0.4865 (OUTLIER) cc_final: 0.4420 (tp) REVERT: M 10 GLN cc_start: 0.0659 (mt0) cc_final: -0.0858 (tp40) outliers start: 61 outliers final: 41 residues processed: 176 average time/residue: 0.1960 time to fit residues: 62.0511 Evaluate side-chains 155 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 96 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 3 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 419 optimal weight: 30.0000 chunk 389 optimal weight: 50.0000 chunk 51 optimal weight: 0.5980 chunk 405 optimal weight: 20.0000 chunk 340 optimal weight: 30.0000 chunk 391 optimal weight: 40.0000 chunk 240 optimal weight: 5.9990 chunk 432 optimal weight: 7.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 148 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.124203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.089367 restraints weight = 141855.163| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 5.27 r_work: 0.3387 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 37098 Z= 0.391 Angle : 0.807 22.128 50550 Z= 0.404 Chirality : 0.050 0.544 5806 Planarity : 0.005 0.058 6413 Dihedral : 6.707 59.494 5893 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer: Outliers : 2.39 % Allowed : 7.85 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.82 (0.12), residues: 4517 helix: -0.07 (0.19), residues: 673 sheet: -1.03 (0.14), residues: 1217 loop : -1.63 (0.11), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 815 TYR 0.033 0.002 TYR C 789 PHE 0.036 0.003 PHE A1062 TRP 0.027 0.002 TRP G 36 HIS 0.046 0.003 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00859 (37002) covalent geometry : angle 0.79117 (50313) SS BOND : bond 0.00424 ( 51) SS BOND : angle 1.19648 ( 102) hydrogen bonds : bond 0.04562 ( 1200) hydrogen bonds : angle 6.49137 ( 3165) link_BETA1-4 : bond 0.00702 ( 15) link_BETA1-4 : angle 2.63762 ( 45) link_NAG-ASN : bond 0.01065 ( 30) link_NAG-ASN : angle 3.25556 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 115 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8589 (mp10) cc_final: 0.8135 (mt0) REVERT: A 200 TYR cc_start: 0.7943 (m-10) cc_final: 0.7737 (m-80) REVERT: A 1138 TYR cc_start: 0.8489 (t80) cc_final: 0.8116 (t80) REVERT: B 177 MET cc_start: 0.6343 (mtm) cc_final: 0.5156 (tpp) REVERT: B 697 MET cc_start: 0.8262 (ttm) cc_final: 0.7799 (mtp) REVERT: B 855 PHE cc_start: 0.7926 (m-10) cc_final: 0.7181 (m-10) REVERT: C 66 HIS cc_start: 0.7498 (p-80) cc_final: 0.6694 (p-80) REVERT: C 200 TYR cc_start: 0.7831 (m-10) cc_final: 0.7485 (m-80) REVERT: C 817 PHE cc_start: 0.8207 (t80) cc_final: 0.7974 (t80) REVERT: C 1029 MET cc_start: 0.9308 (tpp) cc_final: 0.9047 (tpp) REVERT: C 1138 TYR cc_start: 0.8477 (t80) cc_final: 0.8061 (t80) REVERT: K 70 ILE cc_start: 0.1475 (OUTLIER) cc_final: 0.1068 (mp) REVERT: D 10 GLN cc_start: -0.0129 (mt0) cc_final: -0.1113 (tp40) REVERT: D 12 VAL cc_start: 0.3983 (OUTLIER) cc_final: 0.3593 (m) REVERT: D 49 TYR cc_start: 0.5268 (m-80) cc_final: 0.4946 (m-80) REVERT: E 64 PHE cc_start: 0.5131 (p90) cc_final: 0.4711 (p90) REVERT: L 70 ILE cc_start: 0.1325 (OUTLIER) cc_final: 0.0882 (mp) REVERT: N 10 GLN cc_start: 0.0423 (mt0) cc_final: -0.0787 (tp40) REVERT: N 19 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6414 (m) REVERT: N 49 TYR cc_start: 0.5324 (m-10) cc_final: 0.4700 (m-80) REVERT: H 108 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: G 34 MET cc_start: 0.5611 (mmm) cc_final: 0.4746 (mtp) REVERT: M 10 GLN cc_start: 0.0185 (mt0) cc_final: -0.1298 (tp40) REVERT: M 12 VAL cc_start: 0.4093 (OUTLIER) cc_final: 0.3698 (m) outliers start: 94 outliers final: 60 residues processed: 197 average time/residue: 0.1982 time to fit residues: 69.8843 Evaluate side-chains 164 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 98 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 76 optimal weight: 0.7980 chunk 352 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 426 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 437 optimal weight: 50.0000 chunk 376 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** M 33 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 = 0.4604 r_free = 0.4604 target = 0.135572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.098921 restraints weight = 132443.404| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.33 r_work: 0.3511 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37098 Z= 0.139 Angle : 0.616 16.489 50550 Z= 0.306 Chirality : 0.044 0.549 5806 Planarity : 0.004 0.049 6413 Dihedral : 5.956 59.124 5893 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 8.21 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.55 (0.12), residues: 4517 helix: 0.36 (0.20), residues: 670 sheet: -1.06 (0.14), residues: 1269 loop : -1.39 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.018 0.001 TYR M 49 PHE 0.020 0.002 PHE C 855 TRP 0.038 0.002 TRP G 36 HIS 0.009 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00300 (37002) covalent geometry : angle 0.59727 (50313) SS BOND : bond 0.00287 ( 51) SS BOND : angle 1.81734 ( 102) hydrogen bonds : bond 0.03547 ( 1200) hydrogen bonds : angle 5.96160 ( 3165) link_BETA1-4 : bond 0.00547 ( 15) link_BETA1-4 : angle 2.39761 ( 45) link_NAG-ASN : bond 0.00463 ( 30) link_NAG-ASN : angle 2.72365 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 114 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8599 (mp10) cc_final: 0.8210 (mt0) REVERT: A 177 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7260 (mpp) REVERT: A 200 TYR cc_start: 0.7803 (m-10) cc_final: 0.7579 (m-80) REVERT: A 697 MET cc_start: 0.7989 (ttm) cc_final: 0.7536 (mtp) REVERT: A 855 PHE cc_start: 0.7771 (m-80) cc_final: 0.7372 (m-80) REVERT: A 1138 TYR cc_start: 0.8537 (t80) cc_final: 0.8189 (t80) REVERT: B 170 TYR cc_start: 0.7416 (t80) cc_final: 0.7140 (t80) REVERT: B 697 MET cc_start: 0.8057 (ttm) cc_final: 0.7810 (mtp) REVERT: B 855 PHE cc_start: 0.7876 (m-10) cc_final: 0.7260 (m-80) REVERT: C 52 GLN cc_start: 0.8522 (mp10) cc_final: 0.8042 (mt0) REVERT: C 66 HIS cc_start: 0.7304 (p-80) cc_final: 0.6386 (p-80) REVERT: C 153 MET cc_start: 0.4844 (tpt) cc_final: 0.4566 (tpt) REVERT: C 200 TYR cc_start: 0.7679 (m-10) cc_final: 0.7394 (m-80) REVERT: C 759 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8308 (t80) REVERT: C 902 MET cc_start: 0.8497 (mmm) cc_final: 0.8254 (mmm) REVERT: C 1138 TYR cc_start: 0.8563 (t80) cc_final: 0.8058 (t80) REVERT: K 70 ILE cc_start: 0.1417 (OUTLIER) cc_final: 0.0924 (mp) REVERT: D 10 GLN cc_start: -0.0245 (mt0) cc_final: -0.1149 (tp40) REVERT: D 12 VAL cc_start: 0.4009 (OUTLIER) cc_final: 0.3621 (m) REVERT: D 49 TYR cc_start: 0.5113 (m-80) cc_final: 0.4784 (m-80) REVERT: E 64 PHE cc_start: 0.5071 (p90) cc_final: 0.4506 (p90) REVERT: N 10 GLN cc_start: 0.0180 (mt0) cc_final: -0.0958 (tp40) REVERT: N 19 THR cc_start: 0.7337 (OUTLIER) cc_final: 0.6661 (m) REVERT: M 10 GLN cc_start: 0.0237 (mt0) cc_final: -0.1277 (tp40) REVERT: M 12 VAL cc_start: 0.4231 (OUTLIER) cc_final: 0.3900 (m) outliers start: 82 outliers final: 56 residues processed: 187 average time/residue: 0.1932 time to fit residues: 64.5456 Evaluate side-chains 162 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 100 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 30.0000 chunk 194 optimal weight: 0.9990 chunk 452 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 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 = 0.4584 r_free = 0.4584 target = 0.134434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.096663 restraints weight = 127334.396| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.52 r_work: 0.3461 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37098 Z= 0.230 Angle : 0.645 16.928 50550 Z= 0.322 Chirality : 0.045 0.533 5806 Planarity : 0.004 0.051 6413 Dihedral : 5.957 58.716 5893 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 1.93 % Allowed : 8.36 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.50 (0.12), residues: 4517 helix: 0.33 (0.19), residues: 672 sheet: -0.86 (0.15), residues: 1177 loop : -1.43 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 87 TYR 0.031 0.002 TYR L 60 PHE 0.022 0.002 PHE C 800 TRP 0.029 0.002 TRP G 36 HIS 0.007 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00505 (37002) covalent geometry : angle 0.62514 (50313) SS BOND : bond 0.00361 ( 51) SS BOND : angle 1.90834 ( 102) hydrogen bonds : bond 0.03689 ( 1200) hydrogen bonds : angle 5.96833 ( 3165) link_BETA1-4 : bond 0.00499 ( 15) link_BETA1-4 : angle 2.45317 ( 45) link_NAG-ASN : bond 0.00639 ( 30) link_NAG-ASN : angle 2.83230 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 111 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8470 (mp10) cc_final: 0.8123 (mt0) REVERT: A 170 TYR cc_start: 0.6793 (t80) cc_final: 0.6582 (t80) REVERT: A 200 TYR cc_start: 0.7939 (m-10) cc_final: 0.7634 (m-80) REVERT: A 697 MET cc_start: 0.8093 (ttm) cc_final: 0.7692 (mtp) REVERT: A 1138 TYR cc_start: 0.8495 (t80) cc_final: 0.8198 (t80) REVERT: B 52 GLN cc_start: 0.8497 (mp10) cc_final: 0.8158 (mt0) REVERT: B 153 MET cc_start: 0.5373 (tpt) cc_final: 0.5118 (ppp) REVERT: B 170 TYR cc_start: 0.7443 (t80) cc_final: 0.7192 (t80) REVERT: B 660 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8561 (m-10) REVERT: B 697 MET cc_start: 0.8152 (ttm) cc_final: 0.7822 (mtp) REVERT: B 855 PHE cc_start: 0.7765 (m-10) cc_final: 0.7199 (m-80) REVERT: C 52 GLN cc_start: 0.8510 (mp10) cc_final: 0.8144 (mt0) REVERT: C 66 HIS cc_start: 0.7455 (p-80) cc_final: 0.6546 (p-80) REVERT: C 153 MET cc_start: 0.5110 (tpt) cc_final: 0.4393 (tpp) REVERT: C 200 TYR cc_start: 0.7809 (m-10) cc_final: 0.7467 (m-80) REVERT: C 902 MET cc_start: 0.8598 (mmm) cc_final: 0.8351 (mmm) REVERT: C 1138 TYR cc_start: 0.8464 (t80) cc_final: 0.8098 (t80) REVERT: K 70 ILE cc_start: 0.1451 (OUTLIER) cc_final: 0.0960 (mp) REVERT: D 10 GLN cc_start: -0.0202 (mt0) cc_final: -0.1219 (tp40) REVERT: D 12 VAL cc_start: 0.4124 (OUTLIER) cc_final: 0.3729 (m) REVERT: D 49 TYR cc_start: 0.5174 (m-80) cc_final: 0.4851 (m-80) REVERT: E 64 PHE cc_start: 0.5119 (p90) cc_final: 0.4638 (p90) REVERT: N 10 GLN cc_start: -0.0059 (mt0) cc_final: -0.1251 (tp40) REVERT: N 19 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.6645 (m) REVERT: N 49 TYR cc_start: 0.5479 (m-10) cc_final: 0.5074 (m-80) REVERT: M 10 GLN cc_start: 0.0305 (mt0) cc_final: -0.1252 (tp40) REVERT: M 12 VAL cc_start: 0.4045 (OUTLIER) cc_final: 0.3651 (m) outliers start: 76 outliers final: 60 residues processed: 181 average time/residue: 0.1968 time to fit residues: 63.6534 Evaluate side-chains 168 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 103 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 384 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 369 optimal weight: 8.9990 chunk 101 optimal weight: 0.4980 chunk 387 optimal weight: 4.9990 chunk 79 optimal weight: 0.0050 chunk 255 optimal weight: 30.0000 chunk 382 optimal weight: 8.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 901 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 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 = 0.4600 r_free = 0.4600 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.098148 restraints weight = 131162.488| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.44 r_work: 0.3537 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37098 Z= 0.140 Angle : 0.588 14.907 50550 Z= 0.292 Chirality : 0.044 0.539 5806 Planarity : 0.004 0.049 6413 Dihedral : 5.567 58.190 5893 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 1.65 % Allowed : 8.72 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.34 (0.12), residues: 4517 helix: 0.58 (0.20), residues: 672 sheet: -0.77 (0.14), residues: 1203 loop : -1.36 (0.12), residues: 2642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 87 TYR 0.016 0.001 TYR C1067 PHE 0.026 0.001 PHE C 855 TRP 0.031 0.002 TRP G 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00305 (37002) covalent geometry : angle 0.56802 (50313) SS BOND : bond 0.00417 ( 51) SS BOND : angle 1.85379 ( 102) hydrogen bonds : bond 0.03366 ( 1200) hydrogen bonds : angle 5.73432 ( 3165) link_BETA1-4 : bond 0.00481 ( 15) link_BETA1-4 : angle 2.33671 ( 45) link_NAG-ASN : bond 0.00463 ( 30) link_NAG-ASN : angle 2.66390 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8424 (mp10) cc_final: 0.8172 (mt0) REVERT: A 54 LEU cc_start: 0.8757 (mt) cc_final: 0.8459 (mt) REVERT: A 200 TYR cc_start: 0.7857 (m-10) cc_final: 0.7563 (m-80) REVERT: A 697 MET cc_start: 0.8005 (ttm) cc_final: 0.7646 (mtp) REVERT: A 1135 ASN cc_start: 0.8454 (t0) cc_final: 0.8244 (t0) REVERT: A 1138 TYR cc_start: 0.8481 (t80) cc_final: 0.8221 (t80) REVERT: B 52 GLN cc_start: 0.8362 (mp10) cc_final: 0.8097 (mt0) REVERT: B 170 TYR cc_start: 0.7412 (t80) cc_final: 0.7187 (t80) REVERT: B 697 MET cc_start: 0.7971 (ttm) cc_final: 0.7702 (mtp) REVERT: B 855 PHE cc_start: 0.7589 (m-10) cc_final: 0.7156 (m-10) REVERT: B 1138 TYR cc_start: 0.8506 (t80) cc_final: 0.8268 (t80) REVERT: C 52 GLN cc_start: 0.8485 (mp10) cc_final: 0.8205 (mt0) REVERT: C 66 HIS cc_start: 0.7317 (p-80) cc_final: 0.6487 (p90) REVERT: C 153 MET cc_start: 0.5109 (tpt) cc_final: 0.4734 (tpp) REVERT: C 200 TYR cc_start: 0.7717 (m-10) cc_final: 0.7315 (m-80) REVERT: C 759 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8249 (t80) REVERT: C 902 MET cc_start: 0.8490 (mmm) cc_final: 0.8188 (mmm) REVERT: C 1138 TYR cc_start: 0.8474 (t80) cc_final: 0.8097 (t80) REVERT: D 10 GLN cc_start: -0.0190 (mt0) cc_final: -0.1136 (tp40) REVERT: D 12 VAL cc_start: 0.4208 (OUTLIER) cc_final: 0.3797 (m) REVERT: D 49 TYR cc_start: 0.4959 (m-80) cc_final: 0.4720 (m-10) REVERT: E 64 PHE cc_start: 0.5041 (p90) cc_final: 0.4607 (p90) REVERT: L 103 MET cc_start: 0.0455 (tpt) cc_final: 0.0147 (tpt) REVERT: N 10 GLN cc_start: 0.0143 (mt0) cc_final: -0.1258 (tp40) REVERT: N 19 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.6536 (m) REVERT: N 49 TYR cc_start: 0.5443 (m-10) cc_final: 0.4981 (m-80) REVERT: M 10 GLN cc_start: 0.0283 (mt0) cc_final: -0.1346 (tp40) REVERT: O 81 MET cc_start: -0.3600 (tpp) cc_final: -0.4038 (tmm) outliers start: 65 outliers final: 56 residues processed: 178 average time/residue: 0.2043 time to fit residues: 64.5707 Evaluate side-chains 165 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 203 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 415 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 322 optimal weight: 0.0980 chunk 429 optimal weight: 30.0000 chunk 223 optimal weight: 0.0670 chunk 200 optimal weight: 0.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 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 = 0.4607 r_free = 0.4607 target = 0.136037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.099264 restraints weight = 131183.862| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.48 r_work: 0.3530 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37098 Z= 0.126 Angle : 0.578 13.703 50550 Z= 0.287 Chirality : 0.044 0.532 5806 Planarity : 0.004 0.047 6413 Dihedral : 5.358 57.973 5893 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 1.53 % Allowed : 8.82 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.23 (0.12), residues: 4517 helix: 0.69 (0.20), residues: 672 sheet: -0.68 (0.14), residues: 1191 loop : -1.30 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 87 TYR 0.029 0.001 TYR K 60 PHE 0.030 0.001 PHE C 855 TRP 0.046 0.002 TRP G 36 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00274 (37002) covalent geometry : angle 0.55999 (50313) SS BOND : bond 0.00261 ( 51) SS BOND : angle 1.61330 ( 102) hydrogen bonds : bond 0.03307 ( 1200) hydrogen bonds : angle 5.60039 ( 3165) link_BETA1-4 : bond 0.00463 ( 15) link_BETA1-4 : angle 2.31603 ( 45) link_NAG-ASN : bond 0.00442 ( 30) link_NAG-ASN : angle 2.61374 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9034 Ramachandran restraints generated. 4517 Oldfield, 0 Emsley, 4517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 108 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8512 (mp10) cc_final: 0.8207 (mt0) REVERT: A 54 LEU cc_start: 0.8749 (mt) cc_final: 0.8453 (mt) REVERT: A 170 TYR cc_start: 0.6638 (t80) cc_final: 0.6395 (t80) REVERT: A 200 TYR cc_start: 0.7688 (m-10) cc_final: 0.7427 (m-80) REVERT: A 237 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7468 (ptm160) REVERT: A 697 MET cc_start: 0.7993 (ttm) cc_final: 0.7595 (mtp) REVERT: A 1138 TYR cc_start: 0.8524 (t80) cc_final: 0.8265 (t80) REVERT: B 52 GLN cc_start: 0.8409 (mp10) cc_final: 0.8119 (mt0) REVERT: B 170 TYR cc_start: 0.7408 (t80) cc_final: 0.7142 (t80) REVERT: B 697 MET cc_start: 0.7949 (ttm) cc_final: 0.7643 (mtp) REVERT: B 855 PHE cc_start: 0.7934 (m-10) cc_final: 0.7488 (m-10) REVERT: B 1138 TYR cc_start: 0.8593 (t80) cc_final: 0.8355 (t80) REVERT: C 52 GLN cc_start: 0.8566 (mp10) cc_final: 0.8333 (mt0) REVERT: C 66 HIS cc_start: 0.7220 (p-80) cc_final: 0.6327 (p90) REVERT: C 153 MET cc_start: 0.4697 (tpt) cc_final: 0.4407 (tpp) REVERT: C 200 TYR cc_start: 0.7643 (m-10) cc_final: 0.7268 (m-80) REVERT: C 759 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8299 (t80) REVERT: C 902 MET cc_start: 0.8493 (mmm) cc_final: 0.8190 (mmm) REVERT: C 1138 TYR cc_start: 0.8531 (t80) cc_final: 0.8137 (t80) REVERT: D 10 GLN cc_start: 0.0102 (mt0) cc_final: -0.0814 (tp40) REVERT: D 12 VAL cc_start: 0.4070 (OUTLIER) cc_final: 0.3634 (m) REVERT: N 10 GLN cc_start: 0.0485 (mt0) cc_final: -0.0961 (tp40) REVERT: N 19 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6629 (m) REVERT: N 49 TYR cc_start: 0.5575 (m-10) cc_final: 0.5169 (m-80) REVERT: M 10 GLN cc_start: 0.0457 (mt0) cc_final: -0.1132 (tp40) REVERT: O 81 MET cc_start: -0.3507 (tpp) cc_final: -0.4097 (tmm) outliers start: 60 outliers final: 49 residues processed: 164 average time/residue: 0.2072 time to fit residues: 60.2664 Evaluate side-chains 157 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 256 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 410 optimal weight: 0.5980 chunk 339 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 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 = 0.4591 r_free = 0.4591 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.093169 restraints weight = 141380.052| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 5.48 r_work: 0.3522 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37098 Z= 0.124 Angle : 0.571 13.320 50550 Z= 0.282 Chirality : 0.044 0.523 5806 Planarity : 0.004 0.047 6413 Dihedral : 5.204 58.224 5893 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.53 % Allowed : 8.90 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.02 % 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: -1.16 (0.12), residues: 4517 helix: 0.79 (0.20), residues: 671 sheet: -0.63 (0.14), residues: 1205 loop : -1.26 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 87 TYR 0.027 0.001 TYR G 60 PHE 0.030 0.001 PHE C 855 TRP 0.041 0.001 TRP G 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00271 (37002) covalent geometry : angle 0.55367 (50313) SS BOND : bond 0.00247 ( 51) SS BOND : angle 1.49103 ( 102) hydrogen bonds : bond 0.03258 ( 1200) hydrogen bonds : angle 5.50715 ( 3165) link_BETA1-4 : bond 0.00478 ( 15) link_BETA1-4 : angle 2.27668 ( 45) link_NAG-ASN : bond 0.00455 ( 30) link_NAG-ASN : angle 2.59901 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14696.69 seconds wall clock time: 250 minutes 41.83 seconds (15041.83 seconds total)