Starting phenix.real_space_refine on Fri Feb 6 21:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8k_46640/02_2026/9d8k_46640.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8k_46640/02_2026/9d8k_46640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d8k_46640/02_2026/9d8k_46640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8k_46640/02_2026/9d8k_46640.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8k_46640/02_2026/9d8k_46640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8k_46640/02_2026/9d8k_46640.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17706 2.51 5 N 4504 2.21 5 O 5431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s 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: 27761 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 9034 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1127, 8837 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 54, 'TRANS': 1072} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1127, 8837 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 54, 'TRANS': 1072} Chain breaks: 2 bond proxies already assigned to first conformer: 8850 Chain: "B" Number of atoms: 8883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1107, 8686 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 54, 'TRANS': 1052} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1107, 8686 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 54, 'TRANS': 1052} Chain breaks: 2 bond proxies already assigned to first conformer: 8697 Chain: "C" Number of atoms: 8918 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1112, 8721 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1112, 8721 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 bond proxies already assigned to first conformer: 8732 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: 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 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: 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 Residues with excluded nonbonded symmetry interactions: 69 residue: pdb=" N AASP A1135 " occ=0.52 ... (14 atoms not shown) pdb=" OD2BASP A1135 " occ=0.48 residue: pdb=" N APRO A1136 " occ=0.52 ... (12 atoms not shown) pdb=" CD BPRO A1136 " occ=0.48 residue: pdb=" N ALEU A1137 " occ=0.52 ... (14 atoms not shown) pdb=" CD2BLEU A1137 " occ=0.48 residue: pdb=" N AGLN A1138 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN A1138 " occ=0.48 residue: pdb=" N ALEU A1139 " occ=0.52 ... (14 atoms not shown) pdb=" CD2BLEU A1139 " occ=0.48 residue: pdb=" N AGLU A1140 " occ=0.52 ... (16 atoms not shown) pdb=" OE2BGLU A1140 " occ=0.48 residue: pdb=" N ALEU A1141 " occ=0.52 ... (14 atoms not shown) pdb=" CD2BLEU A1141 " occ=0.48 residue: pdb=" N AASP A1142 " occ=0.52 ... (14 atoms not shown) pdb=" OD2BASP A1142 " occ=0.48 residue: pdb=" N ASER A1143 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER A1143 " occ=0.48 residue: pdb=" N APHE A1144 " occ=0.52 ... (20 atoms not shown) pdb=" CZ BPHE A1144 " occ=0.48 residue: pdb=" N ALYS A1145 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A1145 " occ=0.48 residue: pdb=" N AGLU A1146 " occ=0.52 ... (16 atoms not shown) pdb=" OE2BGLU A1146 " occ=0.48 ... (remaining 57 not shown) Time building chain proxies: 11.76, per 1000 atoms: 0.42 Number of scatterers: 27761 At special positions: 0 Unit cell: (144.401, 159.794, 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 5431 8.00 N 4504 7.00 C 17706 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=2.04 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=2.02 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 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG A1401 " - " ASN A 612 " " NAG A1402 " - " ASN A 231 " " NAG A1403 " - " ASN A 121 " " NAG A1404 " - " ASN A 163 " " NAG A1405 " - " ASN A 351 " " NAG A1406 " - " ASN A 62 " " NAG B1401 " - " ASN B 328 " " NAG B1402 " - " ASN B 62 " " NAG B1403 " - " ASN B1070 " " NAG B1404 " - " ASN B 231 " " NAG B1405 " - " ASN B 121 " " NAG B1406 " - " ASN B 340 " " NAG B1407 " - " ASN B 612 " " NAG C1401 " - " ASN C 328 " " NAG C1402 " - " ASN C1070 " " NAG C1403 " - " ASN C 62 " " NAG C1404 " - " ASN C 121 " " NAG C1405 " - " ASN C 163 " " NAG C1406 " - " ASN C 612 " " NAG C1407 " - " ASN C 340 " " NAG D 1 " - " ASN A 279 " " NAG E 1 " - " ASN A 705 " " NAG F 1 " - " ASN A 713 " " NAG G 1 " - " ASN A 797 " " NAG H 1 " - " ASN A1094 " " NAG I 1 " - " ASN A1130 " " NAG J 1 " - " ASN A 328 " " NAG K 1 " - " ASN B 705 " " NAG L 1 " - " ASN B 713 " " NAG M 1 " - " ASN B 797 " " NAG N 1 " - " ASN B1094 " " NAG O 1 " - " ASN B 279 " " NAG P 1 " - " ASN B 351 " " NAG Q 1 " - " ASN B1130 " " NAG R 1 " - " ASN C 279 " " NAG S 1 " - " ASN C 705 " " NAG T 1 " - " ASN C 713 " " NAG U 1 " - " ASN C 797 " " NAG V 1 " - " ASN C1094 " " NAG W 1 " - " ASN C1130 " " NAG X 1 " - " ASN C 231 " " NAG Y 1 " - " ASN C 351 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 47 sheets defined 25.9% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.820A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.601A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.506A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) 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 removed outlier: 3.861A pdb=" N LEU A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.586A pdb=" N ILE A 840 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.536A pdb=" N ILE A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.151A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 931 removed outlier: 4.148A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.874A 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 removed outlier: 3.626A pdb=" N ARG A 979 " --> pdb=" O ASP A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1028 removed outlier: 4.359A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1157 removed outlier: 3.752A pdb=" N BHIS A1155 " --> pdb=" O BTYR A1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.669A 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 364 through 369 removed outlier: 4.213A pdb=" N PHE B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.630A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 612 through 623 removed outlier: 3.635A pdb=" N VAL B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 742 through 750 removed outlier: 4.133A pdb=" N LEU B 748 " --> pdb=" O GLU B 744 " (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 756 through 779 removed outlier: 3.581A pdb=" N LYS B 760 " --> pdb=" O CYS B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 909 through 915 Processing helix chain 'B' and resid 915 through 929 Processing helix chain 'B' and resid 929 through 934 Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.017A 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 978 Processing helix chain 'B' and resid 981 through 1028 removed outlier: 4.373A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1157 removed outlier: 3.804A pdb=" N BHIS B1155 " --> pdb=" O BTYR B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.203A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.246A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 733 through 738 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 881 Processing helix chain 'C' and resid 882 through 887 removed outlier: 4.136A pdb=" N GLY C 887 " --> pdb=" O PHE C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.172A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 934 removed outlier: 4.061A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.931A 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: 4.947A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1157 removed outlier: 3.771A 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 removed outlier: 7.365A pdb=" N ASN A 62 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR A 266 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER A 203 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.797A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.637A pdb=" N GLY A 102 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 153 removed outlier: 3.547A pdb=" N VAL A 142 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 316 removed outlier: 6.822A pdb=" N VAL A 591 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN A 314 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY A 589 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 6.932A pdb=" N ASN A 434 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE A 371 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA8, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 539 removed outlier: 5.745A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.184A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 668 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 697 through 700 removed outlier: 6.700A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LYS B 786 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN A 699 " --> pdb=" O LYS B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.707A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 724 removed outlier: 5.884A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 732 Processing sheet with id=AB6, first strand: chain 'A' and resid 783 through 786 Processing sheet with id=AB7, first strand: chain 'A' and resid 1116 through 1121 removed outlier: 4.591A pdb=" N ALA A1083 " --> pdb=" O SER A1119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.551A pdb=" N PHE B 199 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP B 225 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 201 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 56 removed outlier: 6.881A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.588A pdb=" N LEU B 83 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY B 102 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA B 240 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE B 100 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG B 101 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 166 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU B 131 " --> pdb=" O CYS B 164 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS B 164 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 133 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ASN B 162 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 149 through 153 removed outlier: 7.299A pdb=" N LEU B 140 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ARG B 243 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N VAL B 142 " --> pdb=" O ARG B 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.862A pdb=" N VAL B 591 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN B 314 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 589 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.796A pdb=" N GLU B 321 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ASN B 538 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 544 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 571 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 removed outlier: 5.876A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 697 through 698 removed outlier: 6.892A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 707 through 709 Processing sheet with id=AD2, first strand: chain 'B' and resid 714 through 724 removed outlier: 6.112A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.627A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.453A pdb=" N ASN C 62 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR C 266 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 187 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C 203 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.667A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.517A pdb=" N LEU C 140 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 241 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.802A pdb=" N GLY C 102 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 240 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 100 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG C 101 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.915A pdb=" N VAL C 591 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN C 314 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 589 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 644 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE2, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE3, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.546A pdb=" N TYR C 485 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AE6, first strand: chain 'C' and resid 547 through 550 Processing sheet with id=AE7, first strand: chain 'C' and resid 650 through 656 removed outlier: 5.067A pdb=" N THR C 692 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C 654 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.782A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 714 through 724 removed outlier: 6.961A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 731 through 732 Processing sheet with id=AF2, first strand: chain 'C' and resid 1116 through 1121 removed outlier: 4.417A pdb=" N ALA C1083 " --> pdb=" O SER C1119 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 3.52 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: 8663 1.34 - 1.46: 7198 1.46 - 1.58: 12403 1.58 - 1.71: 0 1.71 - 1.83: 153 Bond restraints: 28417 Sorted by residual: bond pdb=" CB CYS B 734 " pdb=" SG CYS B 734 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" N ASN B 62 " pdb=" CA ASN B 62 " ideal model delta sigma weight residual 1.464 1.446 0.018 1.25e-02 6.40e+03 2.07e+00 bond pdb=" CA VAL B 611 " pdb=" CB VAL B 611 " ideal model delta sigma weight residual 1.550 1.539 0.011 1.03e-02 9.43e+03 1.21e+00 bond pdb=" CB ASN B 62 " pdb=" CG ASN B 62 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" C SER C 704 " pdb=" N ASN C 705 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.52e-02 4.33e+03 1.11e+00 ... (remaining 28412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 38135 2.04 - 4.08: 466 4.08 - 6.13: 40 6.13 - 8.17: 8 8.17 - 10.21: 3 Bond angle restraints: 38652 Sorted by residual: angle pdb=" C HIS C 515 " pdb=" N ALA C 516 " pdb=" CA ALA C 516 " ideal model delta sigma weight residual 121.80 132.01 -10.21 2.44e+00 1.68e-01 1.75e+01 angle pdb=" CA ASN C 121 " pdb=" CB ASN C 121 " pdb=" CG ASN C 121 " ideal model delta sigma weight residual 112.60 115.91 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" C2 NAG A1403 " pdb=" N2 NAG A1403 " pdb=" C7 NAG A1403 " ideal model delta sigma weight residual 124.56 134.21 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C2 NAG C1404 " pdb=" N2 NAG C1404 " pdb=" C7 NAG C1404 " ideal model delta sigma weight residual 124.56 134.17 -9.61 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C ILE C 195 " pdb=" N ASP C 196 " pdb=" CA ASP C 196 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 ... (remaining 38647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 15436 18.09 - 36.18: 1668 36.18 - 54.26: 516 54.26 - 72.35: 97 72.35 - 90.44: 45 Dihedral angle restraints: 17762 sinusoidal: 7802 harmonic: 9960 Sorted by residual: dihedral pdb=" CB CYS A1078 " pdb=" SG CYS A1078 " pdb=" SG CYS A1122 " pdb=" CB CYS A1122 " ideal model delta sinusoidal sigma weight residual -86.00 -13.45 -72.55 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS C 658 " pdb=" SG CYS C 658 " pdb=" SG CYS C 667 " pdb=" CB CYS C 667 " ideal model delta sinusoidal sigma weight residual -86.00 -23.77 -62.23 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CA SER B 61 " pdb=" C SER B 61 " pdb=" N ASN B 62 " pdb=" CA ASN B 62 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 17759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4079 0.075 - 0.150: 439 0.150 - 0.225: 9 0.225 - 0.300: 5 0.300 - 0.375: 3 Chirality restraints: 4535 Sorted by residual: chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C1070 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG B1407 " pdb=" ND2 ASN B 612 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2 NAG C1404 " pdb=" C1 NAG C1404 " pdb=" C3 NAG C1404 " pdb=" N2 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 4532 not shown) Planarity restraints: 4939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 62 " -0.041 2.00e-02 2.50e+03 3.80e-02 1.81e+01 pdb=" CG ASN B 62 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 62 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 62 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1402 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 705 " 0.034 2.00e-02 2.50e+03 3.21e-02 1.29e+01 pdb=" CG ASN C 705 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 705 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 705 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 705 " -0.029 2.00e-02 2.50e+03 2.62e-02 8.61e+00 pdb=" CG ASN A 705 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 705 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 705 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.029 2.00e-02 2.50e+03 ... (remaining 4936 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1004 2.71 - 3.26: 26662 3.26 - 3.80: 44717 3.80 - 4.35: 55193 4.35 - 4.90: 95475 Nonbonded interactions: 223051 Sorted by model distance: nonbonded pdb=" OG1 THR A 672 " pdb=" OE1 GLN A 686 " model vdw 2.159 3.040 nonbonded pdb=" NH1 ARG B 354 " pdb=" O PRO C 227 " model vdw 2.176 3.120 nonbonded pdb=" O CYS B 613 " pdb=" OG SER B 617 " model vdw 2.196 3.040 nonbonded pdb=" O SER B 880 " pdb=" OG1 THR B 883 " model vdw 2.201 3.040 nonbonded pdb=" ND1 HIS C 67 " pdb=" OD1 ASP C 261 " model vdw 2.214 3.120 ... (remaining 223046 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 824 or resid 849 through 1134 or resid 1401 thr \ ough 1406)) selection = (chain 'B' and (resid 15 through 1134 or resid 1401 through 1406)) selection = (chain 'C' and (resid 15 through 824 or resid 849 through 1134 or resid 1401 thr \ ough 1406)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'I' selection = chain 'Q' 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=0.48 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: 3.410 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: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 36.190 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.005 0.051 28527 Z= 0.197 Angle : 0.594 12.224 38939 Z= 0.294 Chirality : 0.046 0.375 4535 Planarity : 0.003 0.048 4897 Dihedral : 16.748 90.440 11233 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 4.20 % Allowed : 24.48 % Favored : 71.31 % 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: -0.07 (0.14), residues: 3397 helix: 2.07 (0.18), residues: 835 sheet: -0.11 (0.18), residues: 720 loop : -1.05 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 979 TYR 0.021 0.001 TYR B 168 PHE 0.017 0.001 PHE A 33 TRP 0.014 0.001 TRP B 629 HIS 0.003 0.001 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00471 (28417) covalent geometry : angle 0.55785 (38652) SS BOND : bond 0.00260 ( 43) SS BOND : angle 1.11348 ( 86) hydrogen bonds : bond 0.11081 ( 1158) hydrogen bonds : angle 6.21866 ( 3159) link_BETA1-4 : bond 0.00443 ( 22) link_BETA1-4 : angle 1.27279 ( 66) link_BETA1-6 : bond 0.00242 ( 3) link_BETA1-6 : angle 1.41226 ( 9) link_NAG-ASN : bond 0.00557 ( 42) link_NAG-ASN : angle 3.40465 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 269 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3559 (tmm) cc_final: 0.2921 (ppp) REVERT: A 175 MET cc_start: 0.1211 (mtt) cc_final: 0.0427 (mtt) REVERT: A 188 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6810 (mmt180) REVERT: A 524 LYS cc_start: 0.5728 (pttp) cc_final: 0.5464 (pttm) REVERT: A 615 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 128 LYS cc_start: 0.7356 (mtpp) cc_final: 0.6852 (mmtt) REVERT: B 151 MET cc_start: 0.1407 (pp-130) cc_final: 0.0826 (ptm) REVERT: B 163 ASN cc_start: 0.6407 (t0) cc_final: 0.5966 (t0) REVERT: B 168 TYR cc_start: 0.6702 (t80) cc_final: 0.6471 (t80) REVERT: B 266 TYR cc_start: 0.8369 (m-80) cc_final: 0.8149 (m-80) REVERT: B 344 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6207 (t80) REVERT: B 406 GLN cc_start: 0.7099 (mt0) cc_final: 0.6804 (tt0) REVERT: B 554 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7523 (mttm) REVERT: B 565 ILE cc_start: 0.8516 (tt) cc_final: 0.8191 (mt) REVERT: B 755 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: B 979 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7620 (mtp180) REVERT: C 17 MET cc_start: 0.4963 (mtt) cc_final: 0.4352 (mmm) REVERT: C 33 PHE cc_start: 0.8435 (m-80) cc_final: 0.8164 (m-80) REVERT: C 54 ASP cc_start: 0.7713 (m-30) cc_final: 0.7430 (m-30) REVERT: C 126 PHE cc_start: 0.7092 (m-80) cc_final: 0.6874 (m-80) REVERT: C 235 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7119 (p90) REVERT: C 331 ASN cc_start: 0.5741 (t0) cc_final: 0.5375 (m-40) REVERT: C 393 TYR cc_start: 0.7692 (m-10) cc_final: 0.7487 (m-10) REVERT: C 415 ILE cc_start: 0.6814 (mm) cc_final: 0.6549 (mm) REVERT: C 421 LYS cc_start: 0.7483 (tptt) cc_final: 0.7022 (tptp) REVERT: C 462 GLU cc_start: 0.7507 (tt0) cc_final: 0.7279 (tt0) REVERT: C 489 GLN cc_start: 0.6870 (mp10) cc_final: 0.6584 (mp10) REVERT: C 816 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: C 1080 ASP cc_start: 0.8211 (t0) cc_final: 0.7785 (t0) outliers start: 85 outliers final: 57 residues processed: 336 average time/residue: 0.1586 time to fit residues: 87.6156 Evaluate side-chains 282 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 932 ASP Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 871 SER Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain C residue 1119 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 849 GLN A1001 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 HIS B 910 ASN B1102 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.188397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128104 restraints weight = 71373.032| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 4.02 r_work: 0.3327 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28527 Z= 0.110 Angle : 0.563 11.805 38939 Z= 0.282 Chirality : 0.044 0.351 4535 Planarity : 0.003 0.047 4897 Dihedral : 6.474 82.710 5154 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 3.90 % Allowed : 23.88 % Favored : 72.21 % 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: 3397 helix: 2.27 (0.18), residues: 833 sheet: -0.05 (0.18), residues: 711 loop : -0.99 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 354 TYR 0.019 0.001 TYR C 450 PHE 0.025 0.001 PHE B 819 TRP 0.013 0.001 TRP B 350 HIS 0.006 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00235 (28417) covalent geometry : angle 0.53438 (38652) SS BOND : bond 0.00305 ( 43) SS BOND : angle 1.21590 ( 86) hydrogen bonds : bond 0.03915 ( 1158) hydrogen bonds : angle 5.26752 ( 3159) link_BETA1-4 : bond 0.00493 ( 22) link_BETA1-4 : angle 1.23600 ( 66) link_BETA1-6 : bond 0.00362 ( 3) link_BETA1-6 : angle 1.15881 ( 9) link_NAG-ASN : bond 0.00583 ( 42) link_NAG-ASN : angle 2.89789 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3482 (tmm) cc_final: 0.2953 (ppp) REVERT: A 175 MET cc_start: -0.0598 (mtt) cc_final: -0.1148 (mtm) REVERT: A 188 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6047 (mmt180) REVERT: A 306 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7803 (mm-30) REVERT: A 311 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8247 (mm-40) REVERT: A 615 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: A 946 ASP cc_start: 0.8193 (m-30) cc_final: 0.7731 (m-30) REVERT: B 17 MET cc_start: 0.5374 (pmm) cc_final: 0.2864 (ttp) REVERT: B 128 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7001 (mmtt) REVERT: B 151 MET cc_start: 0.1553 (pp-130) cc_final: 0.0913 (ptm) REVERT: B 163 ASN cc_start: 0.6361 (t0) cc_final: 0.5901 (t0) REVERT: B 339 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: B 344 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6096 (t80) REVERT: B 406 GLN cc_start: 0.7180 (mt0) cc_final: 0.6692 (tt0) REVERT: B 554 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7613 (mttm) REVERT: B 565 ILE cc_start: 0.8566 (tt) cc_final: 0.8224 (mt) REVERT: B 729 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8479 (ptmt) REVERT: B 973 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 975 ASP cc_start: 0.8548 (t0) cc_final: 0.8112 (t0) REVERT: B 979 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7507 (mmm-85) REVERT: B 1088 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: C 17 MET cc_start: 0.5080 (mtt) cc_final: 0.4408 (mmm) REVERT: C 33 PHE cc_start: 0.8441 (m-80) cc_final: 0.8199 (m-80) REVERT: C 126 PHE cc_start: 0.7064 (m-80) cc_final: 0.6843 (m-80) REVERT: C 144 HIS cc_start: 0.3768 (OUTLIER) cc_final: 0.3390 (t70) REVERT: C 235 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7002 (p90) REVERT: C 236 GLN cc_start: 0.8368 (tt0) cc_final: 0.7929 (tt0) REVERT: C 331 ASN cc_start: 0.6092 (t0) cc_final: 0.5728 (m-40) REVERT: C 415 ILE cc_start: 0.7094 (mm) cc_final: 0.6847 (mm) REVERT: C 421 LYS cc_start: 0.7508 (tptt) cc_final: 0.7059 (tptp) REVERT: C 450 TYR cc_start: 0.7674 (p90) cc_final: 0.7288 (p90) REVERT: C 722 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (mm) REVERT: C 1080 ASP cc_start: 0.8348 (t0) cc_final: 0.7932 (t0) REVERT: C 1119 SER cc_start: 0.8826 (t) cc_final: 0.8572 (t) outliers start: 76 outliers final: 39 residues processed: 312 average time/residue: 0.1658 time to fit residues: 86.0443 Evaluate side-chains 276 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 931 GLN Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 203 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 357 ASN A 609 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 HIS B 910 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.187905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125001 restraints weight = 60312.559| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.59 r_work: 0.3343 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28527 Z= 0.113 Angle : 0.569 18.739 38939 Z= 0.281 Chirality : 0.046 0.842 4535 Planarity : 0.003 0.053 4897 Dihedral : 6.026 59.141 5097 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 4.00 % Allowed : 23.78 % Favored : 72.21 % 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: 0.13 (0.14), residues: 3397 helix: 2.30 (0.18), residues: 826 sheet: 0.02 (0.18), residues: 743 loop : -0.95 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.018 0.001 TYR C1063 PHE 0.025 0.001 PHE B 819 TRP 0.010 0.001 TRP B 350 HIS 0.017 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00256 (28417) covalent geometry : angle 0.53104 (38652) SS BOND : bond 0.00291 ( 43) SS BOND : angle 1.50727 ( 86) hydrogen bonds : bond 0.03781 ( 1158) hydrogen bonds : angle 5.10854 ( 3159) link_BETA1-4 : bond 0.00449 ( 22) link_BETA1-4 : angle 1.21051 ( 66) link_BETA1-6 : bond 0.00353 ( 3) link_BETA1-6 : angle 1.17399 ( 9) link_NAG-ASN : bond 0.00562 ( 42) link_NAG-ASN : angle 3.34105 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3402 (tmm) cc_final: 0.2860 (ppp) REVERT: A 175 MET cc_start: -0.0551 (mtt) cc_final: -0.1260 (mtt) REVERT: A 188 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5894 (mmt180) REVERT: A 256 THR cc_start: 0.0901 (OUTLIER) cc_final: 0.0656 (p) REVERT: A 306 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7836 (mm-30) REVERT: A 311 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: A 611 VAL cc_start: 0.8830 (p) cc_final: 0.8616 (m) REVERT: A 615 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: A 946 ASP cc_start: 0.8165 (m-30) cc_final: 0.7733 (m-30) REVERT: A 1041 LYS cc_start: 0.8877 (tptt) cc_final: 0.8405 (mmmt) REVERT: B 17 MET cc_start: 0.5308 (pmm) cc_final: 0.2868 (ttp) REVERT: B 42 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8080 (mmmt) REVERT: B 128 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7060 (mmtt) REVERT: B 151 MET cc_start: 0.1723 (pp-130) cc_final: 0.1015 (ptm) REVERT: B 163 ASN cc_start: 0.6316 (t0) cc_final: 0.5841 (t0) REVERT: B 230 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7211 (pp) REVERT: B 318 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8096 (mm-40) REVERT: B 344 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5993 (t80) REVERT: B 406 GLN cc_start: 0.7233 (mt0) cc_final: 0.6750 (tt0) REVERT: B 554 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7591 (mttm) REVERT: B 565 ILE cc_start: 0.8545 (tt) cc_final: 0.8214 (mt) REVERT: B 570 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: B 729 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8353 (ptpt) REVERT: B 979 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7708 (mmm-85) REVERT: B 1088 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: C 17 MET cc_start: 0.4963 (OUTLIER) cc_final: 0.4319 (mmm) REVERT: C 33 PHE cc_start: 0.8431 (m-80) cc_final: 0.8175 (m-80) REVERT: C 126 PHE cc_start: 0.7062 (m-80) cc_final: 0.6850 (m-80) REVERT: C 132 PHE cc_start: 0.7066 (m-10) cc_final: 0.6843 (m-10) REVERT: C 236 GLN cc_start: 0.8363 (tt0) cc_final: 0.7843 (tt0) REVERT: C 331 ASN cc_start: 0.6156 (t0) cc_final: 0.5851 (m-40) REVERT: C 357 ASN cc_start: 0.7954 (m110) cc_final: 0.7668 (m-40) REVERT: C 415 ILE cc_start: 0.7099 (mm) cc_final: 0.6859 (mm) REVERT: C 421 LYS cc_start: 0.7463 (tptt) cc_final: 0.7007 (tptp) REVERT: C 450 TYR cc_start: 0.7626 (p90) cc_final: 0.7309 (p90) REVERT: C 524 LYS cc_start: 0.7872 (mttt) cc_final: 0.7621 (mttt) REVERT: C 722 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8618 (mm) REVERT: C 1080 ASP cc_start: 0.8311 (t0) cc_final: 0.7869 (t0) REVERT: C 1119 SER cc_start: 0.8821 (t) cc_final: 0.8553 (t) outliers start: 78 outliers final: 48 residues processed: 293 average time/residue: 0.1553 time to fit residues: 76.6106 Evaluate side-chains 281 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 931 GLN Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1068 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 50 optimal weight: 0.0470 chunk 155 optimal weight: 20.0000 chunk 193 optimal weight: 0.4980 chunk 275 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 302 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 576 GLN B 236 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 HIS B 910 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.187623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125863 restraints weight = 85541.239| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.18 r_work: 0.3317 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28527 Z= 0.122 Angle : 0.572 16.616 38939 Z= 0.283 Chirality : 0.046 0.733 4535 Planarity : 0.003 0.045 4897 Dihedral : 5.873 57.349 5088 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 4.67 % Allowed : 22.88 % Favored : 72.45 % 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: 0.14 (0.14), residues: 3397 helix: 2.27 (0.18), residues: 830 sheet: 0.05 (0.18), residues: 728 loop : -0.93 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.018 0.001 TYR C1063 PHE 0.027 0.001 PHE B 819 TRP 0.010 0.001 TRP C 629 HIS 0.004 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00284 (28417) covalent geometry : angle 0.53656 (38652) SS BOND : bond 0.00366 ( 43) SS BOND : angle 1.83301 ( 86) hydrogen bonds : bond 0.03773 ( 1158) hydrogen bonds : angle 5.07220 ( 3159) link_BETA1-4 : bond 0.00444 ( 22) link_BETA1-4 : angle 1.20908 ( 66) link_BETA1-6 : bond 0.00365 ( 3) link_BETA1-6 : angle 1.20562 ( 9) link_NAG-ASN : bond 0.00588 ( 42) link_NAG-ASN : angle 3.12018 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 233 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3458 (tmm) cc_final: 0.2886 (ppp) REVERT: A 151 MET cc_start: 0.2252 (pp-130) cc_final: 0.1312 (ppp) REVERT: A 175 MET cc_start: -0.0559 (mtt) cc_final: -0.1228 (mtm) REVERT: A 188 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6156 (mmt180) REVERT: A 256 THR cc_start: 0.0917 (OUTLIER) cc_final: 0.0690 (p) REVERT: A 306 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7897 (mm-30) REVERT: A 311 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8377 (mm-40) REVERT: A 615 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 946 ASP cc_start: 0.8264 (m-30) cc_final: 0.7823 (m-30) REVERT: B 17 MET cc_start: 0.5404 (pmm) cc_final: 0.2897 (ttp) REVERT: B 42 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8112 (mmmt) REVERT: B 128 LYS cc_start: 0.7525 (mtpp) cc_final: 0.6994 (mmtt) REVERT: B 151 MET cc_start: 0.1726 (pp-130) cc_final: 0.0991 (ptm) REVERT: B 163 ASN cc_start: 0.6388 (t0) cc_final: 0.5902 (t0) REVERT: B 168 TYR cc_start: 0.6891 (t80) cc_final: 0.6645 (t80) REVERT: B 230 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7262 (pp) REVERT: B 344 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5989 (t80) REVERT: B 406 GLN cc_start: 0.7230 (mt0) cc_final: 0.6747 (tt0) REVERT: B 554 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7554 (mttm) REVERT: B 565 ILE cc_start: 0.8546 (tt) cc_final: 0.8222 (mt) REVERT: B 570 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: B 729 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8385 (ptmt) REVERT: B 973 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8627 (mt) REVERT: B 979 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7756 (mmm-85) REVERT: B 1027 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8701 (mt-10) REVERT: C 17 MET cc_start: 0.4921 (OUTLIER) cc_final: 0.4226 (mmm) REVERT: C 33 PHE cc_start: 0.8466 (m-80) cc_final: 0.8195 (m-80) REVERT: C 126 PHE cc_start: 0.7086 (m-80) cc_final: 0.6872 (m-80) REVERT: C 132 PHE cc_start: 0.7112 (m-10) cc_final: 0.6797 (m-10) REVERT: C 235 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6929 (p90) REVERT: C 236 GLN cc_start: 0.8408 (tt0) cc_final: 0.7929 (tt0) REVERT: C 331 ASN cc_start: 0.6258 (t0) cc_final: 0.5989 (m-40) REVERT: C 357 ASN cc_start: 0.7980 (m110) cc_final: 0.7687 (m-40) REVERT: C 415 ILE cc_start: 0.7103 (mm) cc_final: 0.6879 (mm) REVERT: C 421 LYS cc_start: 0.7485 (tptt) cc_final: 0.7042 (tptp) REVERT: C 450 TYR cc_start: 0.7613 (p90) cc_final: 0.7312 (p90) REVERT: C 722 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8645 (mm) REVERT: C 898 MET cc_start: 0.8908 (mmm) cc_final: 0.8497 (tpt) REVERT: C 1027 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: C 1080 ASP cc_start: 0.8340 (t0) cc_final: 0.7891 (t0) REVERT: C 1119 SER cc_start: 0.8832 (t) cc_final: 0.8560 (t) outliers start: 98 outliers final: 56 residues processed: 309 average time/residue: 0.1628 time to fit residues: 85.1662 Evaluate side-chains 293 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 184 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 243 optimal weight: 0.2980 chunk 167 optimal weight: 10.0000 chunk 291 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 248 optimal weight: 0.0670 chunk 68 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 236 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 621 HIS B 910 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.187736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126987 restraints weight = 65953.704| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.68 r_work: 0.3351 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28527 Z= 0.114 Angle : 0.561 15.613 38939 Z= 0.277 Chirality : 0.045 0.601 4535 Planarity : 0.003 0.045 4897 Dihedral : 5.716 56.838 5084 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 4.60 % Allowed : 23.55 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3397 helix: 2.28 (0.18), residues: 831 sheet: 0.06 (0.18), residues: 738 loop : -0.89 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.018 0.001 TYR C1063 PHE 0.027 0.001 PHE B 819 TRP 0.010 0.001 TRP C 629 HIS 0.007 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00263 (28417) covalent geometry : angle 0.52668 (38652) SS BOND : bond 0.00329 ( 43) SS BOND : angle 1.75107 ( 86) hydrogen bonds : bond 0.03683 ( 1158) hydrogen bonds : angle 5.02413 ( 3159) link_BETA1-4 : bond 0.00423 ( 22) link_BETA1-4 : angle 1.17810 ( 66) link_BETA1-6 : bond 0.00376 ( 3) link_BETA1-6 : angle 1.19313 ( 9) link_NAG-ASN : bond 0.00593 ( 42) link_NAG-ASN : angle 3.05310 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 230 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3499 (tmm) cc_final: 0.2955 (ppp) REVERT: A 151 MET cc_start: 0.2230 (pp-130) cc_final: 0.1205 (ppp) REVERT: A 175 MET cc_start: -0.0497 (mtt) cc_final: -0.1097 (mtm) REVERT: A 188 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6114 (mmt180) REVERT: A 306 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7883 (mm-30) REVERT: A 311 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8336 (mm-40) REVERT: A 615 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 946 ASP cc_start: 0.8168 (m-30) cc_final: 0.7733 (m-30) REVERT: B 42 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8115 (mmmt) REVERT: B 128 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7053 (mmtt) REVERT: B 151 MET cc_start: 0.1772 (pp-130) cc_final: 0.0937 (ptm) REVERT: B 163 ASN cc_start: 0.6316 (t0) cc_final: 0.5840 (t0) REVERT: B 230 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7247 (pp) REVERT: B 344 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5916 (t80) REVERT: B 406 GLN cc_start: 0.7269 (mt0) cc_final: 0.7019 (tt0) REVERT: B 540 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7886 (m-40) REVERT: B 554 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7572 (mttm) REVERT: B 565 ILE cc_start: 0.8516 (tt) cc_final: 0.8187 (mt) REVERT: B 570 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: B 729 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8537 (ptmt) REVERT: B 973 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 979 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7726 (mmm-85) REVERT: B 1027 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: C 17 MET cc_start: 0.4977 (OUTLIER) cc_final: 0.4214 (mmm) REVERT: C 33 PHE cc_start: 0.8455 (m-80) cc_final: 0.8175 (m-80) REVERT: C 132 PHE cc_start: 0.7041 (m-10) cc_final: 0.6716 (m-10) REVERT: C 235 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6909 (p90) REVERT: C 331 ASN cc_start: 0.6372 (t0) cc_final: 0.6096 (m-40) REVERT: C 357 ASN cc_start: 0.7907 (m110) cc_final: 0.7610 (m-40) REVERT: C 421 LYS cc_start: 0.7489 (tptt) cc_final: 0.7039 (tptp) REVERT: C 722 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8607 (mm) REVERT: C 816 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: C 898 MET cc_start: 0.8847 (mmm) cc_final: 0.8461 (tpt) REVERT: C 1027 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: C 1080 ASP cc_start: 0.8262 (t0) cc_final: 0.7842 (t0) REVERT: C 1119 SER cc_start: 0.8817 (t) cc_final: 0.8550 (t) outliers start: 95 outliers final: 58 residues processed: 302 average time/residue: 0.1681 time to fit residues: 86.3460 Evaluate side-chains 294 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 910 ASN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1068 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 322 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 621 HIS B 910 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.185038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123238 restraints weight = 66414.446| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.89 r_work: 0.3285 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28527 Z= 0.215 Angle : 0.632 15.114 38939 Z= 0.315 Chirality : 0.047 0.576 4535 Planarity : 0.004 0.045 4897 Dihedral : 6.009 57.109 5083 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 5.10 % Allowed : 22.95 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3397 helix: 1.98 (0.18), residues: 836 sheet: 0.05 (0.18), residues: 703 loop : -1.00 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.025 0.001 TYR C 450 PHE 0.027 0.002 PHE B 166 TRP 0.013 0.001 TRP C 629 HIS 0.005 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00523 (28417) covalent geometry : angle 0.59777 (38652) SS BOND : bond 0.00398 ( 43) SS BOND : angle 2.11709 ( 86) hydrogen bonds : bond 0.04411 ( 1158) hydrogen bonds : angle 5.17973 ( 3159) link_BETA1-4 : bond 0.00375 ( 22) link_BETA1-4 : angle 1.30946 ( 66) link_BETA1-6 : bond 0.00298 ( 3) link_BETA1-6 : angle 1.31285 ( 9) link_NAG-ASN : bond 0.00583 ( 42) link_NAG-ASN : angle 3.10528 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 234 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3417 (tmm) cc_final: 0.2816 (ppp) REVERT: A 115 SER cc_start: 0.6541 (m) cc_final: 0.6070 (p) REVERT: A 151 MET cc_start: 0.2438 (pp-130) cc_final: 0.1337 (ppp) REVERT: A 175 MET cc_start: -0.0230 (mtt) cc_final: -0.0774 (mtt) REVERT: A 188 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6299 (mmt180) REVERT: A 256 THR cc_start: 0.1137 (OUTLIER) cc_final: 0.0915 (p) REVERT: A 306 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8025 (mm-30) REVERT: A 615 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: B 128 LYS cc_start: 0.7559 (mtpp) cc_final: 0.6999 (mmtt) REVERT: B 151 MET cc_start: 0.1798 (pp-130) cc_final: 0.0998 (ptm) REVERT: B 163 ASN cc_start: 0.6411 (t0) cc_final: 0.5886 (t0) REVERT: B 168 TYR cc_start: 0.7035 (t80) cc_final: 0.6803 (t80) REVERT: B 230 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7292 (pp) REVERT: B 344 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6090 (t80) REVERT: B 406 GLN cc_start: 0.7177 (mt0) cc_final: 0.6912 (tt0) REVERT: B 554 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7647 (mttm) REVERT: B 565 ILE cc_start: 0.8528 (tt) cc_final: 0.8179 (mt) REVERT: B 570 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: B 729 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8536 (ptmt) REVERT: B 979 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7753 (mmm-85) REVERT: B 1027 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: C 17 MET cc_start: 0.4911 (OUTLIER) cc_final: 0.4223 (mmm) REVERT: C 33 PHE cc_start: 0.8515 (m-80) cc_final: 0.8201 (m-80) REVERT: C 132 PHE cc_start: 0.7032 (m-10) cc_final: 0.6755 (m-10) REVERT: C 235 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7058 (p90) REVERT: C 331 ASN cc_start: 0.6572 (t0) cc_final: 0.6177 (m-40) REVERT: C 421 LYS cc_start: 0.7511 (tptt) cc_final: 0.7065 (tptp) REVERT: C 493 PHE cc_start: 0.7369 (m-80) cc_final: 0.6867 (m-10) REVERT: C 722 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8759 (mm) REVERT: C 816 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8506 (m-30) REVERT: C 898 MET cc_start: 0.8809 (mmm) cc_final: 0.8563 (tpt) REVERT: C 1027 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: C 1080 ASP cc_start: 0.8353 (t0) cc_final: 0.7894 (t0) outliers start: 110 outliers final: 70 residues processed: 323 average time/residue: 0.1511 time to fit residues: 82.2134 Evaluate side-chains 305 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 221 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 931 GLN Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1027 GLU Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1132 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 139 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 318 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 621 HIS B 910 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126514 restraints weight = 65419.791| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.75 r_work: 0.3336 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28527 Z= 0.116 Angle : 0.568 14.213 38939 Z= 0.282 Chirality : 0.045 0.543 4535 Planarity : 0.003 0.045 4897 Dihedral : 5.805 56.753 5082 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 4.07 % Allowed : 23.88 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3397 helix: 2.16 (0.18), residues: 837 sheet: 0.04 (0.18), residues: 711 loop : -0.97 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.023 0.001 TYR C 450 PHE 0.051 0.001 PHE C 851 TRP 0.010 0.001 TRP C 629 HIS 0.005 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00266 (28417) covalent geometry : angle 0.53476 (38652) SS BOND : bond 0.00330 ( 43) SS BOND : angle 1.71126 ( 86) hydrogen bonds : bond 0.03773 ( 1158) hydrogen bonds : angle 5.00664 ( 3159) link_BETA1-4 : bond 0.00442 ( 22) link_BETA1-4 : angle 1.18266 ( 66) link_BETA1-6 : bond 0.00384 ( 3) link_BETA1-6 : angle 1.19002 ( 9) link_NAG-ASN : bond 0.00590 ( 42) link_NAG-ASN : angle 3.03373 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 223 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3417 (tmm) cc_final: 0.2797 (ppp) REVERT: A 151 MET cc_start: 0.2424 (pp-130) cc_final: 0.1317 (ppp) REVERT: A 175 MET cc_start: -0.0243 (mtt) cc_final: -0.0865 (mtm) REVERT: A 188 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6184 (mmt180) REVERT: A 256 THR cc_start: 0.1023 (OUTLIER) cc_final: 0.0814 (p) REVERT: A 306 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7978 (mm-30) REVERT: A 615 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: B 128 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7047 (mmtt) REVERT: B 151 MET cc_start: 0.1821 (pp-130) cc_final: 0.0923 (ptm) REVERT: B 163 ASN cc_start: 0.6404 (t0) cc_final: 0.5886 (t0) REVERT: B 339 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: B 344 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.5882 (t80) REVERT: B 406 GLN cc_start: 0.7250 (mt0) cc_final: 0.6982 (tt0) REVERT: B 554 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7626 (mttm) REVERT: B 565 ILE cc_start: 0.8481 (tt) cc_final: 0.8127 (mt) REVERT: B 570 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 574 ASP cc_start: 0.7941 (t0) cc_final: 0.7732 (t0) REVERT: B 729 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8536 (ptmt) REVERT: B 973 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 979 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7731 (mmm-85) REVERT: C 17 MET cc_start: 0.4944 (OUTLIER) cc_final: 0.4180 (mmm) REVERT: C 33 PHE cc_start: 0.8488 (m-80) cc_final: 0.8201 (m-80) REVERT: C 235 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7019 (p90) REVERT: C 331 ASN cc_start: 0.6513 (t0) cc_final: 0.6253 (m-40) REVERT: C 421 LYS cc_start: 0.7494 (tptt) cc_final: 0.7048 (tptp) REVERT: C 493 PHE cc_start: 0.7321 (m-80) cc_final: 0.6776 (m-10) REVERT: C 722 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8675 (mm) REVERT: C 816 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: C 898 MET cc_start: 0.8821 (mmm) cc_final: 0.8508 (tpt) REVERT: C 900 TYR cc_start: 0.7651 (m-10) cc_final: 0.7210 (m-80) REVERT: C 1027 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: C 1080 ASP cc_start: 0.8295 (t0) cc_final: 0.7896 (t0) REVERT: C 1119 SER cc_start: 0.8831 (t) cc_final: 0.8575 (t) outliers start: 79 outliers final: 53 residues processed: 282 average time/residue: 0.1497 time to fit residues: 71.5016 Evaluate side-chains 284 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 910 ASN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1132 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 97 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 291 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 23 optimal weight: 30.0000 chunk 217 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1155 HIS B B 236 GLN B 621 HIS B 910 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.186316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127183 restraints weight = 69752.509| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.74 r_work: 0.3310 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28527 Z= 0.168 Angle : 0.603 14.011 38939 Z= 0.299 Chirality : 0.046 0.534 4535 Planarity : 0.003 0.045 4897 Dihedral : 5.879 57.037 5082 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 4.47 % Allowed : 23.58 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.01 (0.14), residues: 3397 helix: 2.05 (0.18), residues: 838 sheet: 0.01 (0.18), residues: 699 loop : -1.01 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 811 TYR 0.024 0.001 TYR C 450 PHE 0.054 0.001 PHE C 851 TRP 0.012 0.001 TRP C 629 HIS 0.005 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00407 (28417) covalent geometry : angle 0.56799 (38652) SS BOND : bond 0.00365 ( 43) SS BOND : angle 2.13282 ( 86) hydrogen bonds : bond 0.04120 ( 1158) hydrogen bonds : angle 5.06036 ( 3159) link_BETA1-4 : bond 0.00394 ( 22) link_BETA1-4 : angle 1.24772 ( 66) link_BETA1-6 : bond 0.00343 ( 3) link_BETA1-6 : angle 1.24810 ( 9) link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 3.03263 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 226 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.3328 (tmm) cc_final: 0.2693 (ppp) REVERT: A 115 SER cc_start: 0.6563 (m) cc_final: 0.6113 (p) REVERT: A 133 GLN cc_start: 0.6251 (tp40) cc_final: 0.5667 (tm-30) REVERT: A 151 MET cc_start: 0.2510 (pp-130) cc_final: 0.1326 (ppp) REVERT: A 175 MET cc_start: -0.0147 (mtt) cc_final: -0.0680 (mtt) REVERT: A 188 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6276 (mmt180) REVERT: A 256 THR cc_start: 0.1245 (OUTLIER) cc_final: 0.1015 (p) REVERT: A 306 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7983 (mm-30) REVERT: A 615 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: B 42 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8140 (mmmt) REVERT: B 128 LYS cc_start: 0.7577 (mtpp) cc_final: 0.7046 (mmtt) REVERT: B 151 MET cc_start: 0.1829 (pp-130) cc_final: 0.0912 (ptm) REVERT: B 163 ASN cc_start: 0.6469 (t0) cc_final: 0.5957 (t0) REVERT: B 339 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6921 (m-10) REVERT: B 344 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5985 (t80) REVERT: B 375 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7309 (mtpp) REVERT: B 406 GLN cc_start: 0.7232 (mt0) cc_final: 0.6963 (tt0) REVERT: B 554 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7668 (mttm) REVERT: B 565 ILE cc_start: 0.8473 (tt) cc_final: 0.8115 (mt) REVERT: B 570 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: B 729 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8536 (ptmt) REVERT: B 979 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7722 (mmm-85) REVERT: C 17 MET cc_start: 0.4929 (OUTLIER) cc_final: 0.4168 (mmm) REVERT: C 33 PHE cc_start: 0.8483 (m-80) cc_final: 0.8180 (m-80) REVERT: C 235 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7034 (p90) REVERT: C 331 ASN cc_start: 0.6672 (t0) cc_final: 0.6350 (m-40) REVERT: C 357 ASN cc_start: 0.7983 (m110) cc_final: 0.7726 (m-40) REVERT: C 421 LYS cc_start: 0.7518 (tptt) cc_final: 0.7067 (tptp) REVERT: C 493 PHE cc_start: 0.7363 (m-80) cc_final: 0.6834 (m-10) REVERT: C 722 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8717 (mm) REVERT: C 816 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: C 898 MET cc_start: 0.8831 (mmm) cc_final: 0.8575 (tpt) REVERT: C 1027 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: C 1080 ASP cc_start: 0.8311 (t0) cc_final: 0.7898 (t0) outliers start: 91 outliers final: 67 residues processed: 298 average time/residue: 0.1603 time to fit residues: 80.6918 Evaluate side-chains 302 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 221 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 933 SER Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 910 ASN Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1132 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 309 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 264 optimal weight: 0.0000 chunk 319 optimal weight: 4.9990 chunk 131 optimal weight: 0.0470 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 overall best weight: 0.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 HIS B 910 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.189213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128294 restraints weight = 55524.577| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.43 r_work: 0.3383 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 28527 Z= 0.100 Angle : 0.558 13.299 38939 Z= 0.276 Chirality : 0.045 0.519 4535 Planarity : 0.003 0.046 4897 Dihedral : 5.636 57.402 5082 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 3.80 % Allowed : 24.38 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3397 helix: 2.20 (0.18), residues: 839 sheet: 0.14 (0.18), residues: 718 loop : -0.95 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 234 TYR 0.023 0.001 TYR C 450 PHE 0.041 0.001 PHE C 851 TRP 0.009 0.001 TRP C 629 HIS 0.005 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00219 (28417) covalent geometry : angle 0.52506 (38652) SS BOND : bond 0.00307 ( 43) SS BOND : angle 1.82228 ( 86) hydrogen bonds : bond 0.03559 ( 1158) hydrogen bonds : angle 4.89444 ( 3159) link_BETA1-4 : bond 0.00436 ( 22) link_BETA1-4 : angle 1.11595 ( 66) link_BETA1-6 : bond 0.00325 ( 3) link_BETA1-6 : angle 1.16157 ( 9) link_NAG-ASN : bond 0.00580 ( 42) link_NAG-ASN : angle 2.95037 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 234 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.3384 (tmm) cc_final: 0.2717 (ppp) REVERT: A 133 GLN cc_start: 0.6160 (tp40) cc_final: 0.5618 (tm-30) REVERT: A 151 MET cc_start: 0.2493 (pp-130) cc_final: 0.1322 (ppp) REVERT: A 175 MET cc_start: -0.0026 (mtt) cc_final: -0.0535 (mtt) REVERT: A 188 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6122 (mmt180) REVERT: A 256 THR cc_start: 0.1244 (OUTLIER) cc_final: 0.1015 (p) REVERT: A 306 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7944 (mm-30) REVERT: A 615 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 42 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8109 (mmmt) REVERT: B 128 LYS cc_start: 0.7555 (mtpp) cc_final: 0.7000 (mmtt) REVERT: B 151 MET cc_start: 0.1653 (pp-130) cc_final: 0.0759 (ptm) REVERT: B 163 ASN cc_start: 0.6471 (t0) cc_final: 0.6000 (t0) REVERT: B 344 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5747 (t80) REVERT: B 375 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7275 (mtpp) REVERT: B 406 GLN cc_start: 0.7242 (mt0) cc_final: 0.6770 (tt0) REVERT: B 554 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7585 (mttm) REVERT: B 565 ILE cc_start: 0.8427 (tt) cc_final: 0.8043 (mt) REVERT: B 570 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: B 574 ASP cc_start: 0.7894 (t0) cc_final: 0.7692 (t0) REVERT: B 729 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8409 (ptmt) REVERT: B 973 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8607 (mt) REVERT: B 979 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7719 (mmm-85) REVERT: C 17 MET cc_start: 0.5019 (OUTLIER) cc_final: 0.4136 (mmm) REVERT: C 33 PHE cc_start: 0.8419 (m-80) cc_final: 0.8128 (m-80) REVERT: C 331 ASN cc_start: 0.6558 (t0) cc_final: 0.6311 (m-40) REVERT: C 357 ASN cc_start: 0.7925 (m110) cc_final: 0.7665 (m-40) REVERT: C 421 LYS cc_start: 0.7482 (tptt) cc_final: 0.7030 (tptp) REVERT: C 493 PHE cc_start: 0.7275 (m-80) cc_final: 0.6725 (m-10) REVERT: C 554 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7444 (mmtm) REVERT: C 898 MET cc_start: 0.8793 (mmm) cc_final: 0.8467 (tpt) REVERT: C 1027 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: C 1080 ASP cc_start: 0.8202 (t0) cc_final: 0.7843 (t0) outliers start: 71 outliers final: 55 residues processed: 287 average time/residue: 0.1534 time to fit residues: 74.7296 Evaluate side-chains 291 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 910 ASN Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 103 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 280 optimal weight: 0.0040 chunk 87 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 45 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 250 optimal weight: 2.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 HIS B 910 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.187310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125962 restraints weight = 66397.134| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.74 r_work: 0.3327 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28527 Z= 0.149 Angle : 0.588 13.329 38939 Z= 0.291 Chirality : 0.046 0.505 4535 Planarity : 0.003 0.045 4897 Dihedral : 5.696 57.172 5082 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 3.87 % Allowed : 24.42 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3397 helix: 2.13 (0.18), residues: 839 sheet: 0.14 (0.18), residues: 696 loop : -0.98 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 234 TYR 0.023 0.001 TYR C 450 PHE 0.046 0.001 PHE C 851 TRP 0.012 0.001 TRP C 629 HIS 0.006 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00357 (28417) covalent geometry : angle 0.55497 (38652) SS BOND : bond 0.00365 ( 43) SS BOND : angle 1.96268 ( 86) hydrogen bonds : bond 0.03896 ( 1158) hydrogen bonds : angle 4.94840 ( 3159) link_BETA1-4 : bond 0.00406 ( 22) link_BETA1-4 : angle 1.20989 ( 66) link_BETA1-6 : bond 0.00382 ( 3) link_BETA1-6 : angle 1.22553 ( 9) link_NAG-ASN : bond 0.00550 ( 42) link_NAG-ASN : angle 2.95792 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 225 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 17 MET cc_start: 0.3422 (tmm) cc_final: 0.1973 (mtt) REVERT: A 133 GLN cc_start: 0.6159 (tp40) cc_final: 0.5640 (tm-30) REVERT: A 151 MET cc_start: 0.2585 (pp-130) cc_final: 0.1419 (ppp) REVERT: A 175 MET cc_start: -0.0069 (mtt) cc_final: -0.0617 (mtt) REVERT: A 188 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6307 (mmt180) REVERT: A 256 THR cc_start: 0.1224 (OUTLIER) cc_final: 0.0999 (p) REVERT: A 306 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7982 (mm-30) REVERT: A 615 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: B 42 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8121 (mmmt) REVERT: B 128 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7050 (mmtt) REVERT: B 151 MET cc_start: 0.1769 (pp-130) cc_final: 0.0837 (ptm) REVERT: B 163 ASN cc_start: 0.6258 (t0) cc_final: 0.5749 (t0) REVERT: B 339 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: B 344 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.5888 (t80) REVERT: B 375 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7310 (mtpp) REVERT: B 406 GLN cc_start: 0.7230 (mt0) cc_final: 0.6753 (tt0) REVERT: B 554 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7641 (mttm) REVERT: B 565 ILE cc_start: 0.8423 (tt) cc_final: 0.8068 (mt) REVERT: B 570 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: B 729 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8535 (ptmt) REVERT: B 979 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7741 (mmm-85) REVERT: C 17 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4216 (mmm) REVERT: C 33 PHE cc_start: 0.8439 (m-80) cc_final: 0.8129 (m-80) REVERT: C 331 ASN cc_start: 0.6609 (t0) cc_final: 0.6329 (m-40) REVERT: C 357 ASN cc_start: 0.7960 (m110) cc_final: 0.7702 (m-40) REVERT: C 421 LYS cc_start: 0.7483 (tptt) cc_final: 0.7031 (tptp) REVERT: C 493 PHE cc_start: 0.7332 (m-80) cc_final: 0.6791 (m-10) REVERT: C 554 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7439 (mmtp) REVERT: C 898 MET cc_start: 0.8826 (mmm) cc_final: 0.8440 (tpt) REVERT: C 1027 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: C 1080 ASP cc_start: 0.8301 (t0) cc_final: 0.7891 (t0) outliers start: 73 outliers final: 56 residues processed: 282 average time/residue: 0.1538 time to fit residues: 73.2129 Evaluate side-chains 288 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 833 TYR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 1068 GLU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 910 ASN Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1027 GLU Chi-restraints excluded: chain C residue 1132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 22 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 193 optimal weight: 0.4980 chunk 240 optimal weight: 0.9990 chunk 309 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 HIS B 910 ASN ** B1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.188860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129844 restraints weight = 70672.527| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.96 r_work: 0.3354 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28527 Z= 0.106 Angle : 0.564 13.011 38939 Z= 0.279 Chirality : 0.045 0.497 4535 Planarity : 0.003 0.046 4897 Dihedral : 5.576 57.398 5082 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 3.60 % Allowed : 24.72 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3397 helix: 2.22 (0.18), residues: 839 sheet: 0.13 (0.18), residues: 719 loop : -0.93 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 234 TYR 0.023 0.001 TYR C 450 PHE 0.037 0.001 PHE C 851 TRP 0.010 0.001 TRP C 629 HIS 0.006 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00240 (28417) covalent geometry : angle 0.53223 (38652) SS BOND : bond 0.00316 ( 43) SS BOND : angle 1.71894 ( 86) hydrogen bonds : bond 0.03571 ( 1158) hydrogen bonds : angle 4.85821 ( 3159) link_BETA1-4 : bond 0.00449 ( 22) link_BETA1-4 : angle 1.12684 ( 66) link_BETA1-6 : bond 0.00403 ( 3) link_BETA1-6 : angle 1.17423 ( 9) link_NAG-ASN : bond 0.00574 ( 42) link_NAG-ASN : angle 2.91516 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8581.89 seconds wall clock time: 147 minutes 12.40 seconds (8832.40 seconds total)