Starting phenix.real_space_refine on Fri Feb 6 22:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8i_46638/02_2026/9d8i_46638.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8i_46638/02_2026/9d8i_46638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d8i_46638/02_2026/9d8i_46638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8i_46638/02_2026/9d8i_46638.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8i_46638/02_2026/9d8i_46638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8i_46638/02_2026/9d8i_46638.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 120 5.16 5 C 17835 2.51 5 N 4531 2.21 5 O 5485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27971 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 9066 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1129, 8857 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 54, 'TRANS': 1074} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1129, 8857 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 54, 'TRANS': 1074} Chain breaks: 2 bond proxies already assigned to first conformer: 8858 Chain: "B" Number of atoms: 8915 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1109, 8706 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 54, 'TRANS': 1054} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1109, 8706 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 54, 'TRANS': 1054} Chain breaks: 2 bond proxies already assigned to first conformer: 8705 Chain: "C" Number of atoms: 8950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1114, 8741 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 54, 'TRANS': 1059} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1114, 8741 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 54, 'TRANS': 1059} Chain breaks: 2 bond proxies already assigned to first conformer: 8740 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 72 residue: pdb=" N ATYR A1134 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR A1134 " occ=0.45 residue: pdb=" N AASP A1135 " occ=0.55 ... (14 atoms not shown) pdb=" OD2BASP A1135 " occ=0.45 residue: pdb=" N APRO A1136 " occ=0.55 ... (12 atoms not shown) pdb=" CD BPRO A1136 " occ=0.45 residue: pdb=" N ALEU A1137 " occ=0.55 ... (14 atoms not shown) pdb=" CD2BLEU A1137 " occ=0.45 residue: pdb=" N AGLN A1138 " occ=0.55 ... (16 atoms not shown) pdb=" NE2BGLN A1138 " occ=0.45 residue: pdb=" N ALEU A1139 " occ=0.55 ... (14 atoms not shown) pdb=" CD2BLEU A1139 " occ=0.45 residue: pdb=" N AGLU A1140 " occ=0.55 ... (16 atoms not shown) pdb=" OE2BGLU A1140 " occ=0.45 residue: pdb=" N ALEU A1141 " occ=0.55 ... (14 atoms not shown) pdb=" CD2BLEU A1141 " occ=0.45 residue: pdb=" N AASP A1142 " occ=0.55 ... (14 atoms not shown) pdb=" OD2BASP A1142 " occ=0.45 residue: pdb=" N ASER A1143 " occ=0.55 ... (10 atoms not shown) pdb=" OG BSER A1143 " occ=0.45 residue: pdb=" N APHE A1144 " occ=0.55 ... (20 atoms not shown) pdb=" CZ BPHE A1144 " occ=0.45 residue: pdb=" N ALYS A1145 " occ=0.55 ... (16 atoms not shown) pdb=" NZ BLYS A1145 " occ=0.45 ... (remaining 60 not shown) Time building chain proxies: 9.77, per 1000 atoms: 0.35 Number of scatterers: 27971 At special positions: 0 Unit cell: (147.333, 159.061, 213.303, 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 120 16.00 O 5485 8.00 N 4531 7.00 C 17835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " 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 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG O 1 " - " FUC O 3 " " NAG P 1 " - " FUC P 3 " " NAG V 1 " - " FUC V 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG A1401 " - " ASN A 340 " " NAG A1402 " - " ASN A 599 " " NAG A1403 " - " ASN A1070 " " NAG A1404 " - " ASN A 612 " " NAG A1405 " - " ASN A 231 " " NAG A1406 " - " ASN A 62 " " NAG A1407 " - " ASN A 121 " " NAG A1408 " - " ASN A 163 " " NAG A1409 " - " ASN A 351 " " NAG B1401 " - " ASN B 599 " " NAG B1402 " - " ASN B1070 " " NAG B1403 " - " ASN B 231 " " NAG B1404 " - " ASN B 121 " " NAG B1405 " - " ASN B 62 " " NAG B1406 " - " ASN B 328 " " NAG B1407 " - " ASN B 340 " " NAG C1401 " - " ASN C 328 " " NAG C1402 " - " ASN C 612 " " NAG C1403 " - " ASN C 231 " " NAG C1404 " - " ASN C 121 " " NAG C1405 " - " ASN C 163 " " NAG C1406 " - " ASN C 340 " " NAG C1407 " - " ASN C 599 " " NAG C1408 " - " ASN C 62 " " NAG D 1 " - " ASN A 279 " " NAG E 1 " - " ASN A 328 " " NAG F 1 " - " ASN A 705 " " NAG G 1 " - " ASN A 713 " " NAG H 1 " - " ASN A 797 " " NAG I 1 " - " ASN A1094 " " NAG J 1 " - " ASN A1130 " " NAG K 1 " - " ASN B 279 " " NAG L 1 " - " ASN B 705 " " NAG M 1 " - " ASN B 713 " " NAG N 1 " - " ASN B 797 " " NAG O 1 " - " ASN B1094 " " NAG P 1 " - " ASN B1130 " " NAG Q 1 " - " ASN B 612 " " NAG R 1 " - " ASN B 351 " " NAG S 1 " - " ASN C 705 " " NAG T 1 " - " ASN C 713 " " NAG U 1 " - " ASN C1070 " " NAG V 1 " - " ASN C1094 " " NAG W 1 " - " ASN C1130 " " NAG X 1 " - " ASN C 351 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 797 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 49 sheets defined 25.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.995A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 754 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.984A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 removed outlier: 4.132A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 4.151A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.618A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1157 removed outlier: 4.067A pdb=" N BHIS A1155 " --> pdb=" O BTYR A1151 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N BSER A1157 " --> pdb=" O BLYS A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.535A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 380 through 387 removed outlier: 4.409A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.533A pdb=" N VAL B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.507A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 883 through 887 removed outlier: 4.015A pdb=" N GLY B 887 " --> pdb=" O PHE B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 908 through 914 removed outlier: 4.042A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 934 removed outlier: 4.122A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.015A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.599A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1156 removed outlier: 3.851A pdb=" N BHIS B1155 " --> pdb=" O BTYR B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.584A pdb=" N VAL C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.674A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 845 through 851 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 893 through 906 Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.045A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 934 removed outlier: 3.977A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 4.189A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.334A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1156 removed outlier: 3.809A pdb=" N BHIS C1155 " --> pdb=" O BTYR C1151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.067A pdb=" N ASN A 62 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR A 266 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER A 203 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 4.269A pdb=" N ALA C 571 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU C 321 " --> pdb=" O CYS C 534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 56 removed outlier: 7.572A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.765A pdb=" N LEU A 140 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 241 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.271A pdb=" N ALA A 240 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 100 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 166 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.707A pdb=" N VAL A 591 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN A 314 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY A 589 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.186A pdb=" N GLU A 321 " --> pdb=" O CYS A 534 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE A 561 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'A' and resid 371 through 377 removed outlier: 7.857A pdb=" N PHE A 371 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASN A 434 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 650 through 651 removed outlier: 5.988A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA A 668 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 697 through 700 removed outlier: 6.528A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS B 786 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN A 699 " --> pdb=" O LYS B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.602A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN A1102 " --> pdb=" O GLU A1107 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A1107 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 714 through 724 removed outlier: 5.921A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.460A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 784 through 786 Processing sheet with id=AC1, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.687A pdb=" N ASN B 62 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR B 266 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER B 203 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 56 removed outlier: 3.956A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.553A pdb=" N LEU B 140 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.054A pdb=" N GLY B 102 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 240 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 100 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG B 101 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 125 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR B 168 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 127 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 166 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL B 129 " --> pdb=" O CYS B 164 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS B 164 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 160 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.701A pdb=" N VAL B 591 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN B 314 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY B 589 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 325 removed outlier: 5.617A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY B 562 " --> pdb=" O ASP B 570 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 removed outlier: 6.801A pdb=" N GLY B 428 " --> pdb=" O CYS B 376 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N CYS B 376 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL B 430 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 374 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 432 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD3, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.008A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AD5, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.601A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 714 through 724 removed outlier: 7.080A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.469A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1077 through 1078 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.357A pdb=" N ASN C 62 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR C 266 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER C 203 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 56 removed outlier: 7.466A pdb=" N THR C 271 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP C 287 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.929A pdb=" N LEU C 140 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 241 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.658A pdb=" N GLN C 236 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP C 103 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C 238 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG C 101 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 166 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.754A pdb=" N VAL C 591 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN C 314 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY C 589 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 450 removed outlier: 3.605A pdb=" N GLN C 489 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.530A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.724A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN C1102 " --> pdb=" O GLU C1107 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU C1107 " --> pdb=" O GLN C1102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 714 through 724 removed outlier: 7.055A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.469A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1116 through 1118 1190 hydrogen bonds defined for protein. 3267 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: 6.55 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8618 1.34 - 1.46: 5529 1.46 - 1.58: 14333 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 28633 Sorted by residual: bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.563 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C5 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C4 NAG S 1 " pdb=" C5 NAG S 1 " ideal model delta sigma weight residual 1.532 1.560 -0.028 2.00e-02 2.50e+03 1.89e+00 bond pdb=" C SER C 704 " pdb=" N ASN C 705 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.42e-02 4.96e+03 1.74e+00 bond pdb=" CG ASN C 279 " pdb=" ND2 ASN C 279 " ideal model delta sigma weight residual 1.328 1.353 -0.025 2.10e-02 2.27e+03 1.41e+00 ... (remaining 28628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 38311 1.90 - 3.81: 535 3.81 - 5.71: 68 5.71 - 7.61: 19 7.61 - 9.52: 10 Bond angle restraints: 38943 Sorted by residual: angle pdb=" C ASN B1130 " pdb=" CA ASN B1130 " pdb=" CB ASN B1130 " ideal model delta sigma weight residual 110.62 118.45 -7.83 1.46e+00 4.69e-01 2.88e+01 angle pdb=" C ALA A 842 " pdb=" CA ALA A 842 " pdb=" CB ALA A 842 " ideal model delta sigma weight residual 116.54 111.02 5.52 1.15e+00 7.56e-01 2.31e+01 angle pdb=" CA LYS C 459 " pdb=" CB LYS C 459 " pdb=" CG LYS C 459 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.35e+01 angle pdb=" C THR A 598 " pdb=" N ASN A 599 " pdb=" CA ASN A 599 " ideal model delta sigma weight residual 121.64 113.91 7.73 2.13e+00 2.20e-01 1.32e+01 angle pdb=" N ASN A 599 " pdb=" CA ASN A 599 " pdb=" CB ASN A 599 " ideal model delta sigma weight residual 110.26 115.60 -5.34 1.49e+00 4.50e-01 1.29e+01 ... (remaining 38938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 16287 17.83 - 35.66: 1271 35.66 - 53.49: 334 53.49 - 71.32: 80 71.32 - 89.15: 21 Dihedral angle restraints: 17993 sinusoidal: 8003 harmonic: 9990 Sorted by residual: dihedral pdb=" CB CYS B 734 " pdb=" SG CYS B 734 " pdb=" SG CYS B 756 " pdb=" CB CYS B 756 " ideal model delta sinusoidal sigma weight residual -86.00 -34.14 -51.86 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CB CYS B1078 " pdb=" SG CYS B1078 " pdb=" SG CYS B1122 " pdb=" CB CYS B1122 " ideal model delta sinusoidal sigma weight residual -86.00 -40.18 -45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CB CYS C 739 " pdb=" SG CYS C 739 " pdb=" SG CYS C 745 " pdb=" CB CYS C 745 " ideal model delta sinusoidal sigma weight residual -86.00 -45.53 -40.47 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 17990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 4555 0.141 - 0.282: 19 0.282 - 0.423: 6 0.423 - 0.565: 2 0.565 - 0.706: 1 Chirality restraints: 4583 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B1130 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1070 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 599 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 4580 not shown) Planarity restraints: 4971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 705 " -0.062 2.00e-02 2.50e+03 5.61e-02 3.93e+01 pdb=" CG ASN C 705 " 0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN C 705 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 705 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 705 " -0.057 2.00e-02 2.50e+03 5.14e-02 3.30e+01 pdb=" CG ASN A 705 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 705 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 705 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1130 " 0.041 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" CG ASN B1130 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B1130 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B1130 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.038 2.00e-02 2.50e+03 ... (remaining 4968 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 660 2.69 - 3.25: 26400 3.25 - 3.80: 44000 3.80 - 4.35: 59520 4.35 - 4.90: 98594 Nonbonded interactions: 229174 Sorted by model distance: nonbonded pdb=" O ALA B 875 " pdb=" OG1 THR B 879 " model vdw 2.143 3.040 nonbonded pdb=" O ALA A 875 " pdb=" OG1 THR A 879 " model vdw 2.169 3.040 nonbonded pdb=" O ALA C 875 " pdb=" OG1 THR C 879 " model vdw 2.196 3.040 nonbonded pdb=" N GLU B 744 " pdb=" OE1 GLU B 744 " model vdw 2.206 3.120 nonbonded pdb=" O GLY A 876 " pdb=" OG SER A 880 " model vdw 2.211 3.040 ... (remaining 229169 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 15 through 825 or resid 849 through 1133 or resid 1401 thr \ ough 1407)) selection = (chain 'B' and (resid 15 through 1133 or resid 1401 through 1407)) selection = (chain 'C' and (resid 15 through 825 or resid 849 through 1133 or resid 1401 thr \ ough 1407)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=0.98 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.250 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28752 Z= 0.122 Angle : 0.644 13.899 39257 Z= 0.308 Chirality : 0.048 0.706 4583 Planarity : 0.003 0.048 4924 Dihedral : 13.899 89.152 11446 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 2.60 % Allowed : 15.98 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3406 helix: 2.17 (0.18), residues: 830 sheet: 0.20 (0.18), residues: 726 loop : -0.94 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 316 TYR 0.021 0.001 TYR B1063 PHE 0.023 0.001 PHE A 91 TRP 0.014 0.001 TRP B 629 HIS 0.002 0.000 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00261 (28633) covalent geometry : angle 0.57085 (38943) SS BOND : bond 0.00155 ( 43) SS BOND : angle 0.60499 ( 86) hydrogen bonds : bond 0.09874 ( 1172) hydrogen bonds : angle 6.15911 ( 3267) link_BETA1-4 : bond 0.00743 ( 23) link_BETA1-4 : angle 1.89479 ( 69) link_BETA1-6 : bond 0.00442 ( 6) link_BETA1-6 : angle 1.32976 ( 18) link_NAG-ASN : bond 0.00889 ( 47) link_NAG-ASN : angle 4.84007 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4205 (tmm) cc_final: 0.3503 (mmt) REVERT: A 54 ASP cc_start: 0.6517 (t70) cc_final: 0.6234 (t70) REVERT: A 200 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6540 (mtmt) REVERT: A 316 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7462 (mtp-110) REVERT: A 318 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (mm-40) REVERT: A 556 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 810 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7815 (mppt) REVERT: A 973 LEU cc_start: 0.8617 (mt) cc_final: 0.8163 (tp) REVERT: B 33 PHE cc_start: 0.7496 (m-80) cc_final: 0.7188 (m-80) REVERT: B 45 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8531 (mpt180) REVERT: B 151 MET cc_start: -0.0439 (ppp) cc_final: -0.1083 (mtm) REVERT: B 377 TYR cc_start: 0.7163 (m-80) cc_final: 0.6833 (m-10) REVERT: B 528 ASN cc_start: 0.7954 (p0) cc_final: 0.7701 (t0) REVERT: B 560 GLN cc_start: 0.7661 (mm110) cc_final: 0.7392 (mm110) REVERT: B 564 ASP cc_start: 0.7838 (t0) cc_final: 0.7528 (t0) REVERT: B 736 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7593 (tmt) REVERT: B 748 LEU cc_start: 0.8793 (mt) cc_final: 0.8579 (mp) REVERT: B 775 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7582 (tp-100) REVERT: B 786 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8499 (mtpt) REVERT: B 810 LYS cc_start: 0.8046 (mptt) cc_final: 0.7471 (mppt) REVERT: B 960 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7633 (ttmt) REVERT: B 980 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7231 (mt) REVERT: B 984 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: B 1013 GLU cc_start: 0.8390 (tt0) cc_final: 0.8125 (tt0) REVERT: B 1041 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8314 (mppt) REVERT: C 93 SER cc_start: 0.7402 (t) cc_final: 0.6929 (p) REVERT: C 194 ASN cc_start: 0.7616 (m-40) cc_final: 0.6522 (p0) REVERT: C 213 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.3605 (t80) REVERT: C 278 GLU cc_start: 0.7747 (pm20) cc_final: 0.7485 (pm20) REVERT: C 311 GLN cc_start: 0.8472 (tt0) cc_final: 0.8093 (tm130) REVERT: C 385 ASN cc_start: 0.8370 (m-40) cc_final: 0.8170 (m-40) REVERT: C 485 TYR cc_start: 0.3828 (OUTLIER) cc_final: 0.2502 (p90) REVERT: C 560 GLN cc_start: 0.5889 (mm-40) cc_final: 0.5337 (tp40) REVERT: C 579 GLU cc_start: 0.7056 (tt0) cc_final: 0.6618 (tt0) REVERT: C 821 LYS cc_start: 0.8428 (mptt) cc_final: 0.8196 (mptm) outliers start: 62 outliers final: 41 residues processed: 262 average time/residue: 0.4957 time to fit residues: 157.6648 Evaluate side-chains 231 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 980 LEU Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 847 CYS Chi-restraints excluded: chain C residue 874 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 951 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 609 GLN B 747 ASN B 903 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.215922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136790 restraints weight = 50228.674| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 4.22 r_work: 0.3165 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28752 Z= 0.114 Angle : 0.614 13.260 39257 Z= 0.293 Chirality : 0.046 0.497 4583 Planarity : 0.004 0.047 4924 Dihedral : 6.873 59.580 5329 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 3.50 % Allowed : 15.31 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3406 helix: 2.32 (0.18), residues: 823 sheet: 0.24 (0.18), residues: 711 loop : -0.91 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 316 TYR 0.019 0.001 TYR B1063 PHE 0.019 0.001 PHE A 66 TRP 0.015 0.001 TRP C 629 HIS 0.009 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00251 (28633) covalent geometry : angle 0.55187 (38943) SS BOND : bond 0.00273 ( 43) SS BOND : angle 0.77086 ( 86) hydrogen bonds : bond 0.03828 ( 1172) hydrogen bonds : angle 5.07948 ( 3267) link_BETA1-4 : bond 0.00658 ( 23) link_BETA1-4 : angle 1.83560 ( 69) link_BETA1-6 : bond 0.00376 ( 6) link_BETA1-6 : angle 1.38504 ( 18) link_NAG-ASN : bond 0.00865 ( 47) link_NAG-ASN : angle 4.31164 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4300 (tmm) cc_final: 0.3738 (mmt) REVERT: A 54 ASP cc_start: 0.6090 (t70) cc_final: 0.5794 (t0) REVERT: A 200 LYS cc_start: 0.6348 (mtmt) cc_final: 0.5645 (mttp) REVERT: A 239 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5625 (tm) REVERT: A 316 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6542 (mtp-110) REVERT: A 565 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 810 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7292 (mppt) REVERT: A 1006 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7883 (mp-120) REVERT: B 33 PHE cc_start: 0.7477 (m-80) cc_final: 0.7175 (m-80) REVERT: B 45 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8265 (mpt180) REVERT: B 54 ASP cc_start: 0.7913 (t70) cc_final: 0.7490 (t70) REVERT: B 151 MET cc_start: -0.0509 (ppp) cc_final: -0.1110 (mtm) REVERT: B 205 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6513 (m90) REVERT: B 377 TYR cc_start: 0.7048 (m-80) cc_final: 0.6670 (m-10) REVERT: B 528 ASN cc_start: 0.7856 (p0) cc_final: 0.7616 (t0) REVERT: B 560 GLN cc_start: 0.7586 (mm110) cc_final: 0.7304 (mm110) REVERT: B 564 ASP cc_start: 0.7577 (t0) cc_final: 0.7269 (t0) REVERT: B 748 LEU cc_start: 0.8573 (mt) cc_final: 0.8348 (mp) REVERT: B 775 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7046 (tp-100) REVERT: B 786 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8164 (mtpt) REVERT: B 810 LYS cc_start: 0.7845 (mptt) cc_final: 0.7233 (mppt) REVERT: B 960 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7159 (ttmt) REVERT: B 984 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: B 1013 GLU cc_start: 0.7888 (tt0) cc_final: 0.7616 (tt0) REVERT: B 1041 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7957 (mppt) REVERT: C 93 SER cc_start: 0.6991 (t) cc_final: 0.6480 (p) REVERT: C 175 MET cc_start: 0.2493 (mmm) cc_final: 0.2270 (mtm) REVERT: C 194 ASN cc_start: 0.7609 (m-40) cc_final: 0.6513 (p0) REVERT: C 246 LEU cc_start: 0.0926 (OUTLIER) cc_final: 0.0104 (pt) REVERT: C 278 GLU cc_start: 0.7723 (pm20) cc_final: 0.7424 (pm20) REVERT: C 311 GLN cc_start: 0.8293 (tt0) cc_final: 0.7557 (tm130) REVERT: C 550 LYS cc_start: 0.7047 (tptt) cc_final: 0.6589 (tptp) REVERT: C 560 GLN cc_start: 0.5635 (mm-40) cc_final: 0.4996 (tp40) REVERT: C 579 GLU cc_start: 0.6776 (tt0) cc_final: 0.6342 (tp30) REVERT: C 612 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6939 (t0) REVERT: C 722 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8565 (mm) REVERT: C 736 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7251 (tpt) REVERT: C 821 LYS cc_start: 0.7814 (mptt) cc_final: 0.7468 (mptm) outliers start: 85 outliers final: 41 residues processed: 261 average time/residue: 0.4785 time to fit residues: 151.0088 Evaluate side-chains 237 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 671 GLN Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 804 ASP Chi-restraints excluded: chain C residue 874 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 43 optimal weight: 50.0000 chunk 186 optimal weight: 1.9990 chunk 112 optimal weight: 30.0000 chunk 268 optimal weight: 9.9990 chunk 311 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 293 optimal weight: 0.0570 chunk 270 optimal weight: 6.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 311 GLN B 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.217550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143020 restraints weight = 54932.808| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.81 r_work: 0.3229 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28752 Z= 0.117 Angle : 0.584 12.738 39257 Z= 0.281 Chirality : 0.046 0.488 4583 Planarity : 0.003 0.048 4924 Dihedral : 6.486 57.752 5291 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 3.93 % Allowed : 15.11 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3406 helix: 2.42 (0.18), residues: 811 sheet: 0.31 (0.18), residues: 708 loop : -0.92 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 979 TYR 0.017 0.001 TYR B1063 PHE 0.028 0.001 PHE B 368 TRP 0.017 0.001 TRP C 629 HIS 0.005 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00267 (28633) covalent geometry : angle 0.52809 (38943) SS BOND : bond 0.00189 ( 43) SS BOND : angle 0.71871 ( 86) hydrogen bonds : bond 0.03809 ( 1172) hydrogen bonds : angle 4.91279 ( 3267) link_BETA1-4 : bond 0.00541 ( 23) link_BETA1-4 : angle 1.69349 ( 69) link_BETA1-6 : bond 0.00333 ( 6) link_BETA1-6 : angle 1.32189 ( 18) link_NAG-ASN : bond 0.00755 ( 47) link_NAG-ASN : angle 4.01285 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 199 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4527 (tmm) cc_final: 0.3876 (mmt) REVERT: A 54 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5936 (t70) REVERT: A 200 LYS cc_start: 0.6736 (mtmt) cc_final: 0.6024 (mtmm) REVERT: A 239 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5503 (tm) REVERT: A 316 ARG cc_start: 0.7500 (ttp-110) cc_final: 0.6884 (mtp-110) REVERT: A 565 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7232 (tp) REVERT: A 810 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8112 (mmtt) REVERT: B 33 PHE cc_start: 0.7623 (m-80) cc_final: 0.7327 (m-80) REVERT: B 45 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8538 (mpt180) REVERT: B 54 ASP cc_start: 0.8103 (t70) cc_final: 0.7652 (t70) REVERT: B 151 MET cc_start: -0.0531 (ppp) cc_final: -0.1139 (mtm) REVERT: B 188 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6013 (mtp85) REVERT: B 377 TYR cc_start: 0.7245 (m-80) cc_final: 0.6870 (m-10) REVERT: B 528 ASN cc_start: 0.7920 (p0) cc_final: 0.7688 (t0) REVERT: B 560 GLN cc_start: 0.7716 (mm110) cc_final: 0.7435 (mm110) REVERT: B 612 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7501 (t0) REVERT: B 748 LEU cc_start: 0.8818 (mt) cc_final: 0.8595 (mp) REVERT: B 775 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7358 (tp-100) REVERT: B 786 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8377 (mtpt) REVERT: B 960 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7521 (ttmt) REVERT: B 984 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: B 1013 GLU cc_start: 0.8178 (tt0) cc_final: 0.7889 (tt0) REVERT: B 1041 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8095 (mppt) REVERT: C 93 SER cc_start: 0.7215 (t) cc_final: 0.6756 (p) REVERT: C 187 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6096 (mt) REVERT: C 194 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.6515 (p0) REVERT: C 213 PHE cc_start: 0.4605 (OUTLIER) cc_final: 0.3343 (t80) REVERT: C 246 LEU cc_start: 0.0946 (OUTLIER) cc_final: 0.0095 (pt) REVERT: C 278 GLU cc_start: 0.7817 (pm20) cc_final: 0.7547 (pm20) REVERT: C 311 GLN cc_start: 0.8499 (tt0) cc_final: 0.7838 (tm-30) REVERT: C 560 GLN cc_start: 0.5867 (mm-40) cc_final: 0.5263 (tp40) REVERT: C 579 GLU cc_start: 0.6839 (tt0) cc_final: 0.6456 (tp30) REVERT: C 612 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7223 (t0) REVERT: C 722 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8676 (mm) REVERT: C 736 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7513 (tpt) REVERT: C 776 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7730 (mt-10) REVERT: C 821 LYS cc_start: 0.8054 (mptt) cc_final: 0.7716 (mptm) REVERT: C 953 GLN cc_start: 0.7970 (tt0) cc_final: 0.7617 (pt0) REVERT: C 990 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7797 (t70) outliers start: 97 outliers final: 48 residues processed: 274 average time/residue: 0.4851 time to fit residues: 162.5437 Evaluate side-chains 252 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 671 GLN Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 943 LYS Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 804 ASP Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 990 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 264 optimal weight: 50.0000 chunk 183 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 306 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 124 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 331 ASN B 747 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.210967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130254 restraints weight = 49567.996| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.02 r_work: 0.3149 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 28752 Z= 0.271 Angle : 0.701 15.087 39257 Z= 0.340 Chirality : 0.050 0.522 4583 Planarity : 0.004 0.044 4924 Dihedral : 6.921 59.652 5289 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 4.49 % Allowed : 14.91 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3406 helix: 1.96 (0.18), residues: 814 sheet: 0.17 (0.18), residues: 721 loop : -1.12 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 325 TYR 0.020 0.002 TYR A 198 PHE 0.023 0.002 PHE B 368 TRP 0.019 0.002 TRP C 629 HIS 0.007 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00667 (28633) covalent geometry : angle 0.64435 (38943) SS BOND : bond 0.00359 ( 43) SS BOND : angle 0.97685 ( 86) hydrogen bonds : bond 0.05137 ( 1172) hydrogen bonds : angle 5.14729 ( 3267) link_BETA1-4 : bond 0.00799 ( 23) link_BETA1-4 : angle 1.86577 ( 69) link_BETA1-6 : bond 0.00254 ( 6) link_BETA1-6 : angle 1.44424 ( 18) link_NAG-ASN : bond 0.00836 ( 47) link_NAG-ASN : angle 4.44412 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 184 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.3740 (mmt) REVERT: A 54 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5946 (t70) REVERT: A 200 LYS cc_start: 0.6481 (mtmt) cc_final: 0.5879 (mtmt) REVERT: A 239 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5725 (tm) REVERT: A 316 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6698 (mtp-110) REVERT: A 565 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7358 (tp) REVERT: A 810 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7450 (mppt) REVERT: A 1001 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: A 1006 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: B 33 PHE cc_start: 0.7458 (m-80) cc_final: 0.7196 (m-80) REVERT: B 151 MET cc_start: -0.0452 (ppp) cc_final: -0.1121 (mtm) REVERT: B 175 MET cc_start: 0.1521 (mmt) cc_final: 0.1307 (mmp) REVERT: B 188 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5909 (mtp85) REVERT: B 377 TYR cc_start: 0.7255 (m-80) cc_final: 0.6886 (m-10) REVERT: B 527 THR cc_start: 0.7692 (m) cc_final: 0.7256 (m) REVERT: B 528 ASN cc_start: 0.7923 (p0) cc_final: 0.7532 (t0) REVERT: B 612 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7372 (t0) REVERT: B 748 LEU cc_start: 0.8729 (mt) cc_final: 0.8500 (mp) REVERT: B 775 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7254 (tp-100) REVERT: B 786 LYS cc_start: 0.8573 (mtpp) cc_final: 0.8199 (mtpt) REVERT: B 864 GLU cc_start: 0.8005 (tt0) cc_final: 0.7329 (mp0) REVERT: B 960 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7383 (ttmt) REVERT: B 984 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: B 1013 GLU cc_start: 0.8062 (tt0) cc_final: 0.7774 (tt0) REVERT: B 1041 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8029 (mppt) REVERT: C 53 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7107 (tp40) REVERT: C 93 SER cc_start: 0.7232 (t) cc_final: 0.6873 (p) REVERT: C 187 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6038 (mt) REVERT: C 194 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.6711 (p0) REVERT: C 213 PHE cc_start: 0.4597 (OUTLIER) cc_final: 0.3404 (t80) REVERT: C 246 LEU cc_start: 0.1130 (OUTLIER) cc_final: 0.0223 (pt) REVERT: C 278 GLU cc_start: 0.7827 (pm20) cc_final: 0.7580 (pm20) REVERT: C 311 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: C 485 TYR cc_start: 0.3611 (OUTLIER) cc_final: 0.2536 (p90) REVERT: C 550 LYS cc_start: 0.6850 (tppt) cc_final: 0.6368 (tptp) REVERT: C 560 GLN cc_start: 0.5770 (mm-40) cc_final: 0.5135 (tp40) REVERT: C 576 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: C 579 GLU cc_start: 0.6795 (tt0) cc_final: 0.6518 (tp30) REVERT: C 722 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8677 (mm) REVERT: C 736 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7120 (tpt) REVERT: C 821 LYS cc_start: 0.7928 (mptt) cc_final: 0.7598 (mptm) REVERT: C 990 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7669 (t70) outliers start: 109 outliers final: 63 residues processed: 265 average time/residue: 0.4906 time to fit residues: 159.7461 Evaluate side-chains 257 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 172 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 671 GLN Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 943 LYS Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1070 ASN Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 213 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.211926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140599 restraints weight = 54393.700| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.52 r_work: 0.3261 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28752 Z= 0.136 Angle : 0.598 13.429 39257 Z= 0.289 Chirality : 0.046 0.519 4583 Planarity : 0.003 0.046 4924 Dihedral : 6.603 59.389 5287 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 3.53 % Allowed : 15.78 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3406 helix: 2.25 (0.18), residues: 804 sheet: 0.22 (0.19), residues: 706 loop : -1.05 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.018 0.001 TYR B1063 PHE 0.023 0.001 PHE B 368 TRP 0.015 0.001 TRP C 629 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00318 (28633) covalent geometry : angle 0.54660 (38943) SS BOND : bond 0.00221 ( 43) SS BOND : angle 0.74249 ( 86) hydrogen bonds : bond 0.04053 ( 1172) hydrogen bonds : angle 4.92234 ( 3267) link_BETA1-4 : bond 0.00596 ( 23) link_BETA1-4 : angle 1.72436 ( 69) link_BETA1-6 : bond 0.00263 ( 6) link_BETA1-6 : angle 1.32733 ( 18) link_NAG-ASN : bond 0.00743 ( 47) link_NAG-ASN : angle 3.85969 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4669 (tmm) cc_final: 0.3771 (mmt) REVERT: A 54 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.6086 (t70) REVERT: A 200 LYS cc_start: 0.6913 (mtmt) cc_final: 0.6169 (mtmm) REVERT: A 239 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5608 (tm) REVERT: A 316 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7056 (mtp-110) REVERT: A 556 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 565 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7357 (tp) REVERT: B 33 PHE cc_start: 0.7687 (m-80) cc_final: 0.7440 (m-80) REVERT: B 45 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8640 (mpt180) REVERT: B 54 ASP cc_start: 0.8319 (t70) cc_final: 0.7804 (t70) REVERT: B 151 MET cc_start: -0.0558 (ppp) cc_final: -0.1198 (mtm) REVERT: B 188 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6181 (mtp85) REVERT: B 194 ASN cc_start: 0.8359 (t0) cc_final: 0.8072 (t0) REVERT: B 221 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: B 377 TYR cc_start: 0.7396 (m-80) cc_final: 0.7052 (m-10) REVERT: B 527 THR cc_start: 0.7897 (m) cc_final: 0.7383 (m) REVERT: B 528 ASN cc_start: 0.7964 (p0) cc_final: 0.7626 (t0) REVERT: B 564 ASP cc_start: 0.7715 (t0) cc_final: 0.7447 (t0) REVERT: B 612 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7544 (t0) REVERT: B 736 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.7703 (tmt) REVERT: B 775 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7477 (tp-100) REVERT: B 786 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8475 (mtpt) REVERT: B 864 GLU cc_start: 0.8381 (tt0) cc_final: 0.7827 (mp0) REVERT: B 960 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7676 (ttmt) REVERT: B 984 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: B 1013 GLU cc_start: 0.8293 (tt0) cc_final: 0.8020 (tt0) REVERT: B 1041 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8189 (mppt) REVERT: C 33 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6101 (t80) REVERT: C 93 SER cc_start: 0.7348 (t) cc_final: 0.6956 (p) REVERT: C 187 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6156 (mt) REVERT: C 194 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.6668 (p0) REVERT: C 278 GLU cc_start: 0.7880 (pm20) cc_final: 0.7654 (pm20) REVERT: C 311 GLN cc_start: 0.8509 (tt0) cc_final: 0.7910 (tm-30) REVERT: C 526 SER cc_start: 0.8511 (p) cc_final: 0.8150 (m) REVERT: C 560 GLN cc_start: 0.5835 (mm-40) cc_final: 0.5268 (tp40) REVERT: C 579 GLU cc_start: 0.6843 (tt0) cc_final: 0.6544 (tp30) REVERT: C 722 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8787 (mm) REVERT: C 736 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7519 (tpt) REVERT: C 776 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7819 (mt-10) REVERT: C 821 LYS cc_start: 0.8208 (mptt) cc_final: 0.7902 (mptm) REVERT: C 990 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7889 (t70) outliers start: 80 outliers final: 44 residues processed: 244 average time/residue: 0.5514 time to fit residues: 162.4819 Evaluate side-chains 237 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 990 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 162 optimal weight: 9.9990 chunk 298 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 287 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 267 optimal weight: 30.0000 chunk 329 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN C 434 ASN C 758 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.211900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136211 restraints weight = 53588.561| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.28 r_work: 0.3170 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28752 Z= 0.181 Angle : 0.620 13.211 39257 Z= 0.302 Chirality : 0.047 0.554 4583 Planarity : 0.004 0.046 4924 Dihedral : 6.675 59.943 5287 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 4.03 % Allowed : 15.75 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3406 helix: 2.12 (0.18), residues: 810 sheet: 0.14 (0.18), residues: 726 loop : -1.11 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.018 0.001 TYR B1063 PHE 0.021 0.001 PHE A 66 TRP 0.017 0.001 TRP C 629 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00443 (28633) covalent geometry : angle 0.57410 (38943) SS BOND : bond 0.00308 ( 43) SS BOND : angle 0.85482 ( 86) hydrogen bonds : bond 0.04446 ( 1172) hydrogen bonds : angle 4.96694 ( 3267) link_BETA1-4 : bond 0.00553 ( 23) link_BETA1-4 : angle 1.70049 ( 69) link_BETA1-6 : bond 0.00230 ( 6) link_BETA1-6 : angle 1.38926 ( 18) link_NAG-ASN : bond 0.00690 ( 47) link_NAG-ASN : angle 3.71408 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 183 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4741 (OUTLIER) cc_final: 0.4136 (tpt) REVERT: A 54 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6063 (t70) REVERT: A 239 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5593 (tm) REVERT: A 316 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.7056 (mtp-110) REVERT: A 556 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 565 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7376 (tp) REVERT: A 1001 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: B 33 PHE cc_start: 0.7632 (m-80) cc_final: 0.7384 (m-80) REVERT: B 45 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8572 (mpt180) REVERT: B 54 ASP cc_start: 0.8343 (t70) cc_final: 0.7854 (t70) REVERT: B 151 MET cc_start: -0.0387 (ppp) cc_final: -0.1029 (mtm) REVERT: B 188 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6142 (mtp85) REVERT: B 194 ASN cc_start: 0.8342 (t0) cc_final: 0.8015 (t0) REVERT: B 195 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7450 (mp) REVERT: B 377 TYR cc_start: 0.7419 (m-80) cc_final: 0.7084 (m-10) REVERT: B 527 THR cc_start: 0.7815 (m) cc_final: 0.7310 (m) REVERT: B 528 ASN cc_start: 0.8009 (p0) cc_final: 0.7577 (t0) REVERT: B 612 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7553 (t0) REVERT: B 775 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7476 (tp-100) REVERT: B 786 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8424 (mtpt) REVERT: B 960 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7649 (ttmt) REVERT: B 984 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: B 1013 GLU cc_start: 0.8298 (tt0) cc_final: 0.8019 (tt0) REVERT: B 1041 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8172 (mppt) REVERT: C 33 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.5924 (t80) REVERT: C 93 SER cc_start: 0.7238 (t) cc_final: 0.6886 (p) REVERT: C 187 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6137 (mt) REVERT: C 194 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.6746 (p0) REVERT: C 213 PHE cc_start: 0.4679 (OUTLIER) cc_final: 0.3448 (t80) REVERT: C 278 GLU cc_start: 0.7886 (pm20) cc_final: 0.7669 (pm20) REVERT: C 311 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 361 ASP cc_start: 0.7798 (t0) cc_final: 0.7378 (t0) REVERT: C 526 SER cc_start: 0.8510 (p) cc_final: 0.8129 (m) REVERT: C 550 LYS cc_start: 0.7094 (tppt) cc_final: 0.6440 (tptp) REVERT: C 560 GLN cc_start: 0.5770 (mm-40) cc_final: 0.5148 (tp40) REVERT: C 722 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8768 (mm) REVERT: C 736 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7419 (tpt) REVERT: C 776 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7822 (mt-10) REVERT: C 821 LYS cc_start: 0.8157 (mptt) cc_final: 0.7838 (mptm) REVERT: C 990 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7880 (t70) outliers start: 95 outliers final: 58 residues processed: 252 average time/residue: 0.4923 time to fit residues: 152.2278 Evaluate side-chains 256 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 177 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 623 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 128 optimal weight: 0.0770 chunk 109 optimal weight: 0.0470 chunk 179 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 200 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.213396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139227 restraints weight = 55636.641| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 4.34 r_work: 0.3180 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28752 Z= 0.129 Angle : 0.601 14.278 39257 Z= 0.289 Chirality : 0.047 0.595 4583 Planarity : 0.003 0.047 4924 Dihedral : 6.600 58.075 5287 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 3.46 % Allowed : 16.41 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3406 helix: 2.31 (0.18), residues: 804 sheet: 0.23 (0.19), residues: 715 loop : -1.04 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 325 TYR 0.018 0.001 TYR B1063 PHE 0.021 0.001 PHE A 66 TRP 0.018 0.001 TRP C 629 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00299 (28633) covalent geometry : angle 0.54808 (38943) SS BOND : bond 0.00210 ( 43) SS BOND : angle 0.72809 ( 86) hydrogen bonds : bond 0.03948 ( 1172) hydrogen bonds : angle 4.84603 ( 3267) link_BETA1-4 : bond 0.00664 ( 23) link_BETA1-4 : angle 1.68042 ( 69) link_BETA1-6 : bond 0.00293 ( 6) link_BETA1-6 : angle 1.31060 ( 18) link_NAG-ASN : bond 0.00716 ( 47) link_NAG-ASN : angle 3.94418 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 180 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4779 (OUTLIER) cc_final: 0.4170 (tpt) REVERT: A 54 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6072 (t70) REVERT: A 200 LYS cc_start: 0.6877 (mtmt) cc_final: 0.6148 (mtmm) REVERT: A 239 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5534 (tm) REVERT: A 316 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7116 (mtp-110) REVERT: A 552 ASN cc_start: 0.7840 (m-40) cc_final: 0.7623 (t0) REVERT: A 556 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 565 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7349 (tp) REVERT: B 33 PHE cc_start: 0.7680 (m-80) cc_final: 0.7430 (m-80) REVERT: B 45 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8620 (mpt180) REVERT: B 54 ASP cc_start: 0.8342 (t70) cc_final: 0.7839 (t70) REVERT: B 151 MET cc_start: -0.0401 (ppp) cc_final: -0.1051 (mtm) REVERT: B 188 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6184 (mtp85) REVERT: B 194 ASN cc_start: 0.8359 (t0) cc_final: 0.8047 (t0) REVERT: B 377 TYR cc_start: 0.7467 (m-80) cc_final: 0.7148 (m-10) REVERT: B 527 THR cc_start: 0.7845 (m) cc_final: 0.7351 (m) REVERT: B 528 ASN cc_start: 0.8002 (p0) cc_final: 0.7603 (t0) REVERT: B 580 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7479 (pp) REVERT: B 612 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7507 (t0) REVERT: B 775 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7488 (tp-100) REVERT: B 786 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8479 (mtpt) REVERT: B 864 GLU cc_start: 0.8419 (tt0) cc_final: 0.7854 (mp0) REVERT: B 960 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7715 (ttmt) REVERT: B 984 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: B 1013 GLU cc_start: 0.8329 (tt0) cc_final: 0.8067 (tt0) REVERT: B 1041 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8192 (mppt) REVERT: C 33 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6061 (t80) REVERT: C 93 SER cc_start: 0.7264 (t) cc_final: 0.6884 (p) REVERT: C 187 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6192 (mt) REVERT: C 194 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.6706 (p0) REVERT: C 311 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: C 361 ASP cc_start: 0.7784 (t0) cc_final: 0.7373 (t0) REVERT: C 526 SER cc_start: 0.8459 (p) cc_final: 0.8133 (m) REVERT: C 560 GLN cc_start: 0.5820 (mm-40) cc_final: 0.5231 (tp40) REVERT: C 722 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8759 (mm) REVERT: C 736 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7495 (tpt) REVERT: C 776 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7818 (mt-10) REVERT: C 821 LYS cc_start: 0.8196 (mptt) cc_final: 0.7889 (mptm) REVERT: C 990 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7893 (t70) outliers start: 78 outliers final: 51 residues processed: 240 average time/residue: 0.4533 time to fit residues: 134.0591 Evaluate side-chains 245 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 990 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 119 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 321 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.210360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134393 restraints weight = 49451.446| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.69 r_work: 0.3141 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 28752 Z= 0.309 Angle : 0.734 16.994 39257 Z= 0.361 Chirality : 0.052 0.632 4583 Planarity : 0.004 0.043 4924 Dihedral : 7.174 59.098 5283 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.58 % Favored : 94.30 % Rotamer: Outliers : 4.39 % Allowed : 15.85 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3406 helix: 1.71 (0.18), residues: 803 sheet: 0.03 (0.18), residues: 725 loop : -1.25 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 325 TYR 0.023 0.002 TYR A 198 PHE 0.022 0.002 PHE B1117 TRP 0.018 0.002 TRP C 629 HIS 0.008 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00759 (28633) covalent geometry : angle 0.68749 (38943) SS BOND : bond 0.00408 ( 43) SS BOND : angle 1.08262 ( 86) hydrogen bonds : bond 0.05510 ( 1172) hydrogen bonds : angle 5.25127 ( 3267) link_BETA1-4 : bond 0.00568 ( 23) link_BETA1-4 : angle 1.90196 ( 69) link_BETA1-6 : bond 0.00195 ( 6) link_BETA1-6 : angle 1.52596 ( 18) link_NAG-ASN : bond 0.00769 ( 47) link_NAG-ASN : angle 4.10810 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 170 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.4256 (tpp) REVERT: A 54 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6139 (t70) REVERT: A 239 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5820 (tm) REVERT: A 316 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7123 (mtp-110) REVERT: A 565 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7534 (tp) REVERT: A 1001 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: B 45 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.6418 (mpp-170) REVERT: B 151 MET cc_start: -0.0460 (ppp) cc_final: -0.1037 (mtm) REVERT: B 188 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6037 (mtp85) REVERT: B 194 ASN cc_start: 0.8332 (t0) cc_final: 0.7973 (t0) REVERT: B 195 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7452 (mp) REVERT: B 205 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.7003 (m90) REVERT: B 221 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: B 377 TYR cc_start: 0.7526 (m-80) cc_final: 0.7190 (m-10) REVERT: B 512 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.4747 (tm-30) REVERT: B 527 THR cc_start: 0.7822 (m) cc_final: 0.7357 (m) REVERT: B 528 ASN cc_start: 0.8025 (p0) cc_final: 0.7519 (t0) REVERT: B 564 ASP cc_start: 0.7835 (t0) cc_final: 0.7513 (t0) REVERT: B 580 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7597 (pp) REVERT: B 736 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.7527 (tmt) REVERT: B 775 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7598 (tp-100) REVERT: B 786 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8450 (mtpt) REVERT: B 960 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7673 (ttmt) REVERT: B 984 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: B 1013 GLU cc_start: 0.8411 (tt0) cc_final: 0.8201 (tt0) REVERT: B 1041 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8238 (mppt) REVERT: C 93 SER cc_start: 0.7361 (t) cc_final: 0.7046 (p) REVERT: C 187 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6197 (mt) REVERT: C 194 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.6896 (p0) REVERT: C 278 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: C 311 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: C 361 ASP cc_start: 0.7906 (t0) cc_final: 0.7477 (t0) REVERT: C 485 TYR cc_start: 0.3165 (OUTLIER) cc_final: 0.2369 (p90) REVERT: C 526 SER cc_start: 0.8501 (p) cc_final: 0.7959 (t) REVERT: C 642 ARG cc_start: 0.8408 (tpt-90) cc_final: 0.7704 (mtp180) REVERT: C 722 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8823 (mm) REVERT: C 736 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7425 (tpt) REVERT: C 776 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7882 (mt-10) REVERT: C 821 LYS cc_start: 0.8185 (mptt) cc_final: 0.7871 (mptm) REVERT: C 990 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8006 (t70) outliers start: 106 outliers final: 61 residues processed: 249 average time/residue: 0.4701 time to fit residues: 143.6840 Evaluate side-chains 251 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 166 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 984 GLU Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 175 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 93 optimal weight: 0.0970 chunk 275 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 125 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN A1102 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B1079 HIS C 357 ASN C 609 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.212152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138387 restraints weight = 54634.170| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.95 r_work: 0.3224 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28752 Z= 0.107 Angle : 0.589 13.251 39257 Z= 0.285 Chirality : 0.046 0.566 4583 Planarity : 0.003 0.046 4924 Dihedral : 6.671 58.733 5283 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 3.16 % Allowed : 17.21 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3406 helix: 2.22 (0.18), residues: 798 sheet: 0.20 (0.19), residues: 703 loop : -1.07 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.019 0.001 TYR B1063 PHE 0.021 0.001 PHE A 66 TRP 0.019 0.001 TRP C 629 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00235 (28633) covalent geometry : angle 0.54119 (38943) SS BOND : bond 0.00212 ( 43) SS BOND : angle 0.72315 ( 86) hydrogen bonds : bond 0.03738 ( 1172) hydrogen bonds : angle 4.85244 ( 3267) link_BETA1-4 : bond 0.00587 ( 23) link_BETA1-4 : angle 1.64565 ( 69) link_BETA1-6 : bond 0.00344 ( 6) link_BETA1-6 : angle 1.27251 ( 18) link_NAG-ASN : bond 0.00678 ( 47) link_NAG-ASN : angle 3.72335 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4637 (tmm) cc_final: 0.4244 (tpp) REVERT: A 54 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.6047 (t70) REVERT: A 66 PHE cc_start: 0.6280 (m-80) cc_final: 0.6078 (m-80) REVERT: A 200 LYS cc_start: 0.6785 (mtmt) cc_final: 0.6065 (mtmm) REVERT: A 239 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5522 (tm) REVERT: A 316 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7137 (mtp-110) REVERT: A 556 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 565 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7364 (tp) REVERT: A 1001 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: B 45 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8594 (mpt180) REVERT: B 54 ASP cc_start: 0.8343 (t70) cc_final: 0.7858 (t70) REVERT: B 151 MET cc_start: -0.0646 (ppp) cc_final: -0.1245 (mtm) REVERT: B 175 MET cc_start: 0.3184 (mmp) cc_final: 0.0742 (ppp) REVERT: B 188 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6082 (mtp85) REVERT: B 194 ASN cc_start: 0.8289 (t0) cc_final: 0.7887 (t0) REVERT: B 221 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 377 TYR cc_start: 0.7405 (m-80) cc_final: 0.7098 (m-10) REVERT: B 528 ASN cc_start: 0.8018 (p0) cc_final: 0.7586 (t0) REVERT: B 560 GLN cc_start: 0.7764 (mm110) cc_final: 0.7518 (mm110) REVERT: B 564 ASP cc_start: 0.7793 (t0) cc_final: 0.7506 (t0) REVERT: B 580 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7504 (pp) REVERT: B 736 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7767 (tmt) REVERT: B 775 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7455 (tp-100) REVERT: B 786 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8498 (mtpp) REVERT: B 960 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7663 (ttmt) REVERT: B 984 GLU cc_start: 0.7607 (mp0) cc_final: 0.7077 (OUTLIER) REVERT: B 1013 GLU cc_start: 0.8309 (tt0) cc_final: 0.8028 (tt0) REVERT: B 1041 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8184 (mppt) REVERT: C 194 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.6694 (p0) REVERT: C 278 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: C 311 GLN cc_start: 0.8565 (tt0) cc_final: 0.7937 (tm-30) REVERT: C 361 ASP cc_start: 0.7740 (t0) cc_final: 0.7342 (t0) REVERT: C 485 TYR cc_start: 0.3192 (OUTLIER) cc_final: 0.2519 (p90) REVERT: C 526 SER cc_start: 0.8444 (p) cc_final: 0.8032 (t) REVERT: C 560 GLN cc_start: 0.5855 (mm-40) cc_final: 0.5173 (tp40) REVERT: C 722 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 736 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7452 (tpt) REVERT: C 776 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7810 (mt-10) REVERT: C 821 LYS cc_start: 0.8226 (mptt) cc_final: 0.7940 (mptm) REVERT: C 990 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7864 (t70) outliers start: 69 outliers final: 45 residues processed: 234 average time/residue: 0.4420 time to fit residues: 127.6016 Evaluate side-chains 238 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 990 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 62 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 273 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 231 optimal weight: 0.3980 chunk 189 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN C 357 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.213006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137808 restraints weight = 48622.187| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.56 r_work: 0.3251 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28752 Z= 0.107 Angle : 0.567 12.538 39257 Z= 0.274 Chirality : 0.045 0.533 4583 Planarity : 0.003 0.047 4924 Dihedral : 6.350 59.244 5280 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 2.63 % Allowed : 17.88 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3406 helix: 2.37 (0.18), residues: 812 sheet: 0.27 (0.19), residues: 704 loop : -1.00 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 354 TYR 0.017 0.001 TYR B1063 PHE 0.023 0.001 PHE A 66 TRP 0.017 0.001 TRP C 629 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00243 (28633) covalent geometry : angle 0.52338 (38943) SS BOND : bond 0.00187 ( 43) SS BOND : angle 0.73533 ( 86) hydrogen bonds : bond 0.03626 ( 1172) hydrogen bonds : angle 4.71358 ( 3267) link_BETA1-4 : bond 0.00585 ( 23) link_BETA1-4 : angle 1.61055 ( 69) link_BETA1-6 : bond 0.00309 ( 6) link_BETA1-6 : angle 1.29366 ( 18) link_NAG-ASN : bond 0.00599 ( 47) link_NAG-ASN : angle 3.48260 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.4701 (tmm) cc_final: 0.4109 (tpt) REVERT: A 54 ASP cc_start: 0.6298 (t70) cc_final: 0.6026 (t70) REVERT: A 200 LYS cc_start: 0.6762 (mtmt) cc_final: 0.6077 (mttp) REVERT: A 239 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5361 (tm) REVERT: A 316 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7127 (mtp-110) REVERT: A 565 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7294 (tp) REVERT: A 1001 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: B 54 ASP cc_start: 0.8244 (t70) cc_final: 0.7868 (t70) REVERT: B 151 MET cc_start: -0.0604 (ppp) cc_final: -0.1232 (mtm) REVERT: B 175 MET cc_start: 0.3389 (mmp) cc_final: 0.0801 (ppp) REVERT: B 188 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6168 (mtp85) REVERT: B 194 ASN cc_start: 0.8302 (t0) cc_final: 0.7905 (t0) REVERT: B 377 TYR cc_start: 0.7418 (m-80) cc_final: 0.7134 (m-10) REVERT: B 527 THR cc_start: 0.7849 (m) cc_final: 0.7382 (m) REVERT: B 528 ASN cc_start: 0.8035 (p0) cc_final: 0.7574 (t0) REVERT: B 564 ASP cc_start: 0.7708 (t0) cc_final: 0.7467 (t0) REVERT: B 612 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7366 (t0) REVERT: B 775 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7450 (tp-100) REVERT: B 786 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8503 (mtpp) REVERT: B 960 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7681 (ttmt) REVERT: B 984 GLU cc_start: 0.7647 (mp0) cc_final: 0.7050 (OUTLIER) REVERT: B 1013 GLU cc_start: 0.8262 (tt0) cc_final: 0.7992 (tt0) REVERT: B 1041 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8159 (mppt) REVERT: C 194 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.6620 (p0) REVERT: C 311 GLN cc_start: 0.8505 (tt0) cc_final: 0.7914 (tm-30) REVERT: C 361 ASP cc_start: 0.7691 (t0) cc_final: 0.7304 (t0) REVERT: C 526 SER cc_start: 0.8435 (p) cc_final: 0.8044 (t) REVERT: C 549 THR cc_start: 0.7545 (m) cc_final: 0.7135 (t) REVERT: C 560 GLN cc_start: 0.5979 (mm-40) cc_final: 0.5309 (tp40) REVERT: C 722 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8712 (mm) REVERT: C 736 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7419 (tpt) REVERT: C 821 LYS cc_start: 0.8257 (mptt) cc_final: 0.7971 (mptm) REVERT: C 990 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7772 (t70) outliers start: 53 outliers final: 38 residues processed: 224 average time/residue: 0.4802 time to fit residues: 131.5403 Evaluate side-chains 226 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 1041 LYS Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 990 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 286 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 331 optimal weight: 0.0170 chunk 250 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 206 optimal weight: 0.6980 chunk 264 optimal weight: 30.0000 chunk 271 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 240 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.211563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141327 restraints weight = 58237.158| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.92 r_work: 0.3239 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28752 Z= 0.146 Angle : 0.593 13.493 39257 Z= 0.288 Chirality : 0.046 0.549 4583 Planarity : 0.003 0.047 4924 Dihedral : 6.344 59.901 5274 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 2.80 % Allowed : 17.78 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3406 helix: 2.31 (0.18), residues: 811 sheet: 0.24 (0.19), residues: 705 loop : -1.03 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 573 TYR 0.018 0.001 TYR B1063 PHE 0.022 0.001 PHE A 66 TRP 0.019 0.001 TRP C 629 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00349 (28633) covalent geometry : angle 0.55045 (38943) SS BOND : bond 0.00219 ( 43) SS BOND : angle 0.75828 ( 86) hydrogen bonds : bond 0.04009 ( 1172) hydrogen bonds : angle 4.79660 ( 3267) link_BETA1-4 : bond 0.00560 ( 23) link_BETA1-4 : angle 1.61102 ( 69) link_BETA1-6 : bond 0.00283 ( 6) link_BETA1-6 : angle 1.30192 ( 18) link_NAG-ASN : bond 0.00602 ( 47) link_NAG-ASN : angle 3.51526 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12894.49 seconds wall clock time: 219 minutes 19.53 seconds (13159.53 seconds total)