Starting phenix.real_space_refine on Fri Feb 6 21:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8j_46639/02_2026/9d8j_46639_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8j_46639/02_2026/9d8j_46639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d8j_46639/02_2026/9d8j_46639_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8j_46639/02_2026/9d8j_46639_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d8j_46639/02_2026/9d8j_46639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8j_46639/02_2026/9d8j_46639.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 17646 2.51 5 N 4488 2.21 5 O 5412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s 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: 27666 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" 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: "B" 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: "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: 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: "I" 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 69 residue: pdb=" N AASP A1135 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP A1135 " occ=0.51 residue: pdb=" N APRO A1136 " occ=0.49 ... (12 atoms not shown) pdb=" CD BPRO A1136 " occ=0.51 residue: pdb=" N ALEU A1137 " occ=0.49 ... (14 atoms not shown) pdb=" CD2BLEU A1137 " occ=0.51 residue: pdb=" N AGLN A1138 " occ=0.49 ... (16 atoms not shown) pdb=" NE2BGLN A1138 " occ=0.51 residue: pdb=" N ALEU A1139 " occ=0.49 ... (14 atoms not shown) pdb=" CD2BLEU A1139 " occ=0.51 residue: pdb=" N AGLU A1140 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU A1140 " occ=0.51 residue: pdb=" N ALEU A1141 " occ=0.49 ... (14 atoms not shown) pdb=" CD2BLEU A1141 " occ=0.51 residue: pdb=" N AASP A1142 " occ=0.49 ... (14 atoms not shown) pdb=" OD2BASP A1142 " occ=0.51 residue: pdb=" N ASER A1143 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER A1143 " occ=0.51 residue: pdb=" N APHE A1144 " occ=0.49 ... (20 atoms not shown) pdb=" CZ BPHE A1144 " occ=0.51 residue: pdb=" N ALYS A1145 " occ=0.49 ... (16 atoms not shown) pdb=" NZ BLYS A1145 " occ=0.51 residue: pdb=" N AGLU A1146 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU A1146 " occ=0.51 ... (remaining 57 not shown) Time building chain proxies: 11.48, per 1000 atoms: 0.41 Number of scatterers: 27666 At special positions: 0 Unit cell: (149.532, 159.061, 194.978, 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 5412 8.00 N 4488 7.00 C 17646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.02 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.02 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.02 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=2.02 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=2.02 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=2.02 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 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAG T 1 " - " FUC T 3 " NAG-ASN " NAG A1401 " - " ASN A 328 " " NAG A1402 " - " ASN A 340 " " NAG A1403 " - " ASN A1070 " " NAG A1404 " - " ASN A1094 " " NAG A1405 " - " ASN A 612 " " NAG A1406 " - " ASN A 231 " " NAG A1407 " - " ASN A 62 " " NAG A1408 " - " ASN A 121 " " NAG A1409 " - " ASN A 163 " " NAG B1401 " - " ASN B 328 " " NAG B1402 " - " ASN B 340 " " NAG B1403 " - " ASN B1070 " " NAG B1404 " - " ASN B1094 " " NAG B1405 " - " ASN B 612 " " NAG B1406 " - " ASN B 231 " " NAG B1407 " - " ASN B 62 " " NAG B1408 " - " ASN B 121 " " NAG B1409 " - " ASN B 163 " " NAG C1401 " - " ASN C 328 " " NAG C1402 " - " ASN C 340 " " NAG C1403 " - " ASN C1070 " " NAG C1404 " - " ASN C1094 " " NAG C1405 " - " ASN C 612 " " NAG C1406 " - " ASN C 231 " " NAG C1407 " - " ASN C 62 " " NAG C1408 " - " ASN C 121 " " NAG C1409 " - " ASN C 163 " " 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 A1130 " " NAG I 1 " - " ASN A 351 " " NAG J 1 " - " ASN B 279 " " NAG K 1 " - " ASN B 705 " " NAG L 1 " - " ASN B 713 " " NAG M 1 " - " ASN B 797 " " NAG N 1 " - " ASN B1130 " " NAG O 1 " - " ASN B 351 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN C 705 " " NAG R 1 " - " ASN C 713 " " NAG S 1 " - " ASN C 797 " " NAG T 1 " - " ASN C1130 " " NAG U 1 " - " ASN C 351 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 2.3 seconds 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 26.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.555A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.701A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.318A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 754 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.702A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 883 through 887 removed outlier: 4.058A pdb=" N GLY A 887 " --> pdb=" O PHE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 908 through 914 removed outlier: 4.043A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 934 removed outlier: 4.167A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.956A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.585A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1157 removed outlier: 3.637A pdb=" N AGLU A1147 " --> pdb=" O ASER A1143 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N BHIS A1155 " --> pdb=" O BTYR A1151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N BSER A1157 " --> pdb=" O BLYS A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.556A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.701A pdb=" N VAL B 364 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.318A 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 498 through 501 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 845 through 852 removed outlier: 3.702A pdb=" N ASN B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 883 through 887 removed outlier: 4.057A pdb=" N GLY B 887 " --> pdb=" O PHE B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 908 through 914 removed outlier: 4.042A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 934 removed outlier: 4.167A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.956A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.585A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1157 removed outlier: 3.636A pdb=" N AGLU B1147 " --> pdb=" O ASER B1143 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N BHIS B1155 " --> pdb=" O BTYR B1151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N BSER B1157 " --> pdb=" O BLYS B1153 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.555A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.701A pdb=" N VAL C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.319A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 845 through 852 removed outlier: 3.702A pdb=" N ASN C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 883 through 887 removed outlier: 4.058A 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 914 removed outlier: 4.042A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 934 removed outlier: 4.167A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.957A 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: 4.585A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1157 removed outlier: 3.637A pdb=" N AGLU C1147 " --> pdb=" O ASER C1143 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N BHIS C1155 " --> pdb=" O BTYR C1151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N BSER C1157 " --> pdb=" O BLYS C1153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.617A pdb=" N ASN A 62 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR A 266 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N SER A 203 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.575A pdb=" N GLY C 562 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 56 removed outlier: 3.876A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.653A pdb=" N LEU A 140 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.848A pdb=" N GLY A 102 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 240 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 100 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 166 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.401A pdb=" N ILE A 309 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A 595 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLN A 311 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 593 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 325 removed outlier: 5.387A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 562 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 561 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 650 through 656 removed outlier: 5.945A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL A 652 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A 668 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 697 through 700 removed outlier: 6.789A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LYS B 786 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASN A 699 " --> pdb=" O LYS B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.748A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN A1102 " --> pdb=" O GLU A1107 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU A1107 " --> pdb=" O GLN A1102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 714 through 724 removed outlier: 7.050A pdb=" N GLY A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A1051 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1057 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1059 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A1047 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A1061 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.464A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 783 through 786 Processing sheet with id=AC1, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.617A pdb=" N ASN B 62 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR B 266 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SER B 203 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 56 removed outlier: 3.876A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.654A pdb=" N LEU B 140 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.848A pdb=" N GLY B 102 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 240 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 100 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG B 101 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 166 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.401A pdb=" N ILE B 309 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR B 595 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLN B 311 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 593 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 325 removed outlier: 5.387A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 562 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B 561 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AD1, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AD2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD4, first strand: chain 'B' and resid 650 through 656 removed outlier: 5.945A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL B 652 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 697 through 700 removed outlier: 6.829A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LYS C 786 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN B 699 " --> pdb=" O LYS C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.749A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN B1102 " --> pdb=" O GLU B1107 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU B1107 " --> pdb=" O GLN B1102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 714 through 724 removed outlier: 7.050A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.464A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.617A pdb=" N ASN C 62 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR C 266 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N SER C 203 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 56 removed outlier: 3.876A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.652A pdb=" N LEU C 140 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.848A pdb=" N GLY C 102 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 240 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 100 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG C 101 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C 166 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.401A pdb=" N ILE C 309 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR C 595 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN C 311 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL C 593 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE8, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF2, first strand: chain 'C' and resid 650 through 656 removed outlier: 5.946A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL C 652 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.748A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN C1102 " --> pdb=" O GLU C1107 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU C1107 " --> pdb=" O GLN C1102 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 714 through 724 removed outlier: 7.051A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.464A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1116 through 1118 1202 hydrogen bonds defined for protein. 3309 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: 7.41 Time building geometry restraints manager: 3.30 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: 8456 1.34 - 1.45: 5020 1.45 - 1.57: 14691 1.57 - 1.69: 0 1.69 - 1.81: 153 Bond restraints: 28320 Sorted by residual: bond pdb=" CB CYS B 734 " pdb=" SG CYS B 734 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.84e+00 bond pdb=" CB CYS A 734 " pdb=" SG CYS A 734 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.82e+00 bond pdb=" CB CYS C 734 " pdb=" SG CYS C 734 " ideal model delta sigma weight residual 1.808 1.744 0.064 3.30e-02 9.18e+02 3.82e+00 bond pdb=" CB CYS A 756 " pdb=" SG CYS A 756 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB CYS B 756 " pdb=" SG CYS B 756 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.75e+00 ... (remaining 28315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 37757 1.87 - 3.74: 655 3.74 - 5.61: 87 5.61 - 7.47: 12 7.47 - 9.34: 12 Bond angle restraints: 38523 Sorted by residual: angle pdb=" C ASN C 62 " pdb=" CA ASN C 62 " pdb=" CB ASN C 62 " ideal model delta sigma weight residual 111.82 117.27 -5.45 1.38e+00 5.25e-01 1.56e+01 angle pdb=" C ASN A 62 " pdb=" CA ASN A 62 " pdb=" CB ASN A 62 " ideal model delta sigma weight residual 111.82 117.26 -5.44 1.38e+00 5.25e-01 1.55e+01 angle pdb=" C ASN B 62 " pdb=" CA ASN B 62 " pdb=" CB ASN B 62 " ideal model delta sigma weight residual 111.82 117.23 -5.41 1.38e+00 5.25e-01 1.54e+01 angle pdb=" CG ARG C 234 " pdb=" CD ARG C 234 " pdb=" NE ARG C 234 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.95e+00 angle pdb=" CG ARG A 234 " pdb=" CD ARG A 234 " pdb=" NE ARG A 234 " ideal model delta sigma weight residual 112.00 118.91 -6.91 2.20e+00 2.07e-01 9.88e+00 ... (remaining 38518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15528 17.96 - 35.92: 1574 35.92 - 53.88: 463 53.88 - 71.84: 93 71.84 - 89.80: 33 Dihedral angle restraints: 17691 sinusoidal: 7758 harmonic: 9933 Sorted by residual: dihedral pdb=" CB CYS B 739 " pdb=" SG CYS B 739 " pdb=" SG CYS B 745 " pdb=" CB CYS B 745 " ideal model delta sinusoidal sigma weight residual -86.00 -43.15 -42.85 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 739 " pdb=" SG CYS A 739 " pdb=" SG CYS A 745 " pdb=" CB CYS A 745 " ideal model delta sinusoidal sigma weight residual -86.00 -43.19 -42.81 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS C 739 " pdb=" SG CYS C 739 " pdb=" SG CYS C 745 " pdb=" CB CYS C 745 " ideal model delta sinusoidal sigma weight residual -86.00 -43.20 -42.80 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 17688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4080 0.079 - 0.157: 420 0.157 - 0.236: 12 0.236 - 0.315: 6 0.315 - 0.394: 3 Chirality restraints: 4521 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" ND2 ASN C 62 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1 NAG A1407 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C1 NAG B1407 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 4518 not shown) Planarity restraints: 4926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 62 " -0.031 2.00e-02 2.50e+03 3.22e-02 1.29e+01 pdb=" CG ASN B 62 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 62 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 62 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG B1407 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 62 " -0.031 2.00e-02 2.50e+03 3.20e-02 1.28e+01 pdb=" CG ASN A 62 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 62 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 62 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 62 " -0.031 2.00e-02 2.50e+03 3.20e-02 1.28e+01 pdb=" CG ASN C 62 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 62 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 62 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.035 2.00e-02 2.50e+03 ... (remaining 4923 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 524 2.68 - 3.23: 25435 3.23 - 3.79: 43367 3.79 - 4.34: 59644 4.34 - 4.90: 98869 Nonbonded interactions: 227839 Sorted by model distance: nonbonded pdb=" OE1 GLN A 318 " pdb=" OG1 THR A 626 " model vdw 2.123 3.040 nonbonded pdb=" OE1 GLN C 318 " pdb=" OG1 THR C 626 " model vdw 2.123 3.040 nonbonded pdb=" OE1 GLN B 318 " pdb=" OG1 THR B 626 " model vdw 2.123 3.040 nonbonded pdb=" O ALA C 875 " pdb=" OG1 THR C 879 " model vdw 2.168 3.040 nonbonded pdb=" O ALA A 875 " pdb=" OG1 THR A 879 " model vdw 2.168 3.040 ... (remaining 227834 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 1134 or resid 1401 through 1409)) selection = (chain 'B' and (resid 15 through 1134 or resid 1401 through 1409)) selection = (chain 'C' and (resid 15 through 1134 or resid 1401 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'N' selection = chain 'T' } 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=0.49 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: 3.150 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: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 35.720 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 0.065 28428 Z= 0.196 Angle : 0.684 15.433 38805 Z= 0.339 Chirality : 0.047 0.394 4521 Planarity : 0.004 0.049 4881 Dihedral : 16.032 89.802 11181 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.34 % Allowed : 21.33 % Favored : 76.33 % 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: 3387 helix: 1.65 (0.18), residues: 792 sheet: 0.29 (0.18), residues: 699 loop : -0.65 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 234 TYR 0.020 0.001 TYR C1063 PHE 0.016 0.002 PHE C1117 TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00470 (28320) covalent geometry : angle 0.61845 (38523) SS BOND : bond 0.00433 ( 42) SS BOND : angle 2.07949 ( 84) hydrogen bonds : bond 0.09326 ( 1184) hydrogen bonds : angle 6.35944 ( 3309) link_BETA1-4 : bond 0.00202 ( 18) link_BETA1-4 : angle 1.30944 ( 54) link_BETA1-6 : bond 0.00104 ( 3) link_BETA1-6 : angle 1.22484 ( 9) link_NAG-ASN : bond 0.01007 ( 45) link_NAG-ASN : angle 4.66167 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.6832 (m-80) cc_final: 0.6579 (m-80) REVERT: A 205 HIS cc_start: 0.7497 (m90) cc_final: 0.7209 (m-70) REVERT: A 218 SER cc_start: 0.8784 (m) cc_final: 0.8253 (p) REVERT: A 521 CYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6203 (m) REVERT: A 528 ASN cc_start: 0.8359 (t0) cc_final: 0.7740 (m110) REVERT: A 552 ASN cc_start: 0.7513 (p0) cc_final: 0.6934 (m110) REVERT: A 560 GLN cc_start: 0.7379 (mm110) cc_final: 0.7093 (mm-40) REVERT: A 772 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7834 (ttpt) REVERT: A 1088 GLU cc_start: 0.8098 (tp30) cc_final: 0.7799 (tt0) REVERT: A 1097 HIS cc_start: 0.8425 (m170) cc_final: 0.8152 (m90) REVERT: B 17 MET cc_start: 0.2930 (tpp) cc_final: 0.2701 (tmm) REVERT: B 29 TYR cc_start: 0.6864 (m-80) cc_final: 0.6632 (m-80) REVERT: B 86 ASN cc_start: 0.7870 (m-40) cc_final: 0.7644 (m110) REVERT: B 205 HIS cc_start: 0.7380 (m90) cc_final: 0.7115 (m-70) REVERT: B 218 SER cc_start: 0.8806 (m) cc_final: 0.8183 (p) REVERT: B 234 ARG cc_start: 0.7534 (mtp85) cc_final: 0.6827 (ttm110) REVERT: B 521 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.6067 (m) REVERT: B 528 ASN cc_start: 0.8332 (t0) cc_final: 0.7840 (m110) REVERT: B 552 ASN cc_start: 0.7440 (p0) cc_final: 0.6683 (m-40) REVERT: B 560 GLN cc_start: 0.7452 (mm110) cc_final: 0.7027 (mm-40) REVERT: B 567 ASP cc_start: 0.8148 (m-30) cc_final: 0.7185 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7569 (tt0) cc_final: 0.6875 (mt-10) REVERT: B 1088 GLU cc_start: 0.8139 (tp30) cc_final: 0.7854 (tt0) REVERT: B 1097 HIS cc_start: 0.8497 (m170) cc_final: 0.8296 (m90) REVERT: C 218 SER cc_start: 0.8686 (m) cc_final: 0.8061 (p) REVERT: C 234 ARG cc_start: 0.7416 (mtp85) cc_final: 0.6711 (ttm-80) REVERT: C 560 GLN cc_start: 0.7623 (mm110) cc_final: 0.7178 (mm-40) REVERT: C 567 ASP cc_start: 0.8084 (m-30) cc_final: 0.7049 (t0) REVERT: C 570 ASP cc_start: 0.7392 (t0) cc_final: 0.6921 (t0) REVERT: C 772 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7879 (tttm) REVERT: C 1088 GLU cc_start: 0.8108 (tp30) cc_final: 0.7855 (tp30) REVERT: C 1097 HIS cc_start: 0.8482 (m170) cc_final: 0.8282 (m90) REVERT: C 1134 TYR cc_start: 0.8357 (m-80) cc_final: 0.8069 (m-80) outliers start: 49 outliers final: 31 residues processed: 257 average time/residue: 0.5400 time to fit residues: 169.0276 Evaluate side-chains 208 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 959 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 318 GLN A 536 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 318 GLN B 536 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 311 GLN C 318 GLN C 528 ASN C 536 ASN C 609 GLN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.215400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138660 restraints weight = 59032.376| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.58 r_work: 0.3271 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28428 Z= 0.123 Angle : 0.589 9.342 38805 Z= 0.295 Chirality : 0.044 0.255 4521 Planarity : 0.004 0.048 4881 Dihedral : 6.284 57.105 5069 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.04 % Allowed : 20.63 % Favored : 76.33 % 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: 0.32 (0.14), residues: 3387 helix: 2.14 (0.18), residues: 774 sheet: 0.21 (0.17), residues: 744 loop : -0.61 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 234 TYR 0.018 0.001 TYR A1063 PHE 0.013 0.001 PHE B1117 TRP 0.015 0.001 TRP C 629 HIS 0.002 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00274 (28320) covalent geometry : angle 0.55214 (38523) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.67195 ( 84) hydrogen bonds : bond 0.03992 ( 1184) hydrogen bonds : angle 5.35684 ( 3309) link_BETA1-4 : bond 0.00338 ( 18) link_BETA1-4 : angle 1.18781 ( 54) link_BETA1-6 : bond 0.00300 ( 3) link_BETA1-6 : angle 1.17854 ( 9) link_NAG-ASN : bond 0.00844 ( 45) link_NAG-ASN : angle 3.21911 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.6928 (m-80) cc_final: 0.6586 (m-80) REVERT: A 188 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7467 (mtp180) REVERT: A 218 SER cc_start: 0.8762 (m) cc_final: 0.8215 (p) REVERT: A 528 ASN cc_start: 0.8295 (t0) cc_final: 0.7672 (m110) REVERT: A 552 ASN cc_start: 0.7562 (p0) cc_final: 0.6879 (m110) REVERT: A 579 GLU cc_start: 0.7439 (tt0) cc_final: 0.6622 (mt-10) REVERT: A 729 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8269 (mtmm) REVERT: A 1088 GLU cc_start: 0.8148 (tp30) cc_final: 0.7882 (tt0) REVERT: A 1097 HIS cc_start: 0.8460 (m170) cc_final: 0.8164 (m90) REVERT: A 1134 TYR cc_start: 0.8350 (m-80) cc_final: 0.8061 (m-80) REVERT: B 29 TYR cc_start: 0.7124 (m-80) cc_final: 0.6767 (m-80) REVERT: B 86 ASN cc_start: 0.7903 (m-40) cc_final: 0.7533 (m110) REVERT: B 205 HIS cc_start: 0.7405 (m90) cc_final: 0.7200 (m-70) REVERT: B 218 SER cc_start: 0.8798 (m) cc_final: 0.8200 (p) REVERT: B 234 ARG cc_start: 0.7439 (mtp85) cc_final: 0.6825 (ttp-110) REVERT: B 528 ASN cc_start: 0.8276 (t0) cc_final: 0.7784 (m110) REVERT: B 552 ASN cc_start: 0.7345 (p0) cc_final: 0.6661 (m110) REVERT: B 560 GLN cc_start: 0.7476 (mm110) cc_final: 0.7070 (mm-40) REVERT: B 567 ASP cc_start: 0.8169 (m-30) cc_final: 0.7094 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7535 (tt0) cc_final: 0.6901 (mt-10) REVERT: B 729 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8458 (mtmm) REVERT: B 1088 GLU cc_start: 0.8153 (tp30) cc_final: 0.7842 (tt0) REVERT: B 1109 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: C 151 MET cc_start: 0.1690 (OUTLIER) cc_final: 0.1487 (pmt) REVERT: C 218 SER cc_start: 0.8625 (m) cc_final: 0.7979 (p) REVERT: C 234 ARG cc_start: 0.7353 (mtp85) cc_final: 0.6739 (ttm-80) REVERT: C 377 TYR cc_start: 0.6393 (m-80) cc_final: 0.6045 (m-10) REVERT: C 521 CYS cc_start: 0.6377 (OUTLIER) cc_final: 0.6144 (m) REVERT: C 560 GLN cc_start: 0.7601 (mm110) cc_final: 0.7199 (mm-40) REVERT: C 579 GLU cc_start: 0.7546 (tt0) cc_final: 0.6758 (mt-10) REVERT: C 729 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8430 (mtmt) REVERT: C 973 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (mp) REVERT: C 1088 GLU cc_start: 0.8155 (tp30) cc_final: 0.7922 (tp30) REVERT: C 1134 TYR cc_start: 0.8305 (m-80) cc_final: 0.8059 (m-80) outliers start: 70 outliers final: 27 residues processed: 246 average time/residue: 0.5431 time to fit residues: 162.9964 Evaluate side-chains 192 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 279 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 314 optimal weight: 0.0570 chunk 198 optimal weight: 4.9990 chunk 156 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 307 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 331 ASN A 536 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN B 331 ASN B 536 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 311 GLN C 318 GLN C 528 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.207525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134551 restraints weight = 56164.555| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.05 r_work: 0.3238 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28428 Z= 0.203 Angle : 0.638 14.593 38805 Z= 0.316 Chirality : 0.046 0.267 4521 Planarity : 0.004 0.053 4881 Dihedral : 6.066 57.701 5039 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.68 % Allowed : 19.83 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3387 helix: 1.96 (0.18), residues: 774 sheet: 0.16 (0.17), residues: 744 loop : -0.72 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 234 TYR 0.019 0.001 TYR A1063 PHE 0.015 0.001 PHE A1117 TRP 0.015 0.002 TRP C 629 HIS 0.005 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00494 (28320) covalent geometry : angle 0.59795 (38523) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.78520 ( 84) hydrogen bonds : bond 0.04656 ( 1184) hydrogen bonds : angle 5.35950 ( 3309) link_BETA1-4 : bond 0.00186 ( 18) link_BETA1-4 : angle 1.35498 ( 54) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.36113 ( 9) link_NAG-ASN : bond 0.00808 ( 45) link_NAG-ASN : angle 3.48245 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 172 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.6968 (m-80) cc_final: 0.6613 (m-80) REVERT: A 188 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7428 (mtp180) REVERT: A 218 SER cc_start: 0.8754 (m) cc_final: 0.8203 (p) REVERT: A 528 ASN cc_start: 0.8333 (t0) cc_final: 0.7701 (m110) REVERT: A 543 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 560 GLN cc_start: 0.7476 (mm110) cc_final: 0.7126 (mm-40) REVERT: A 579 GLU cc_start: 0.7513 (tt0) cc_final: 0.6714 (mt-10) REVERT: A 729 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8371 (mttt) REVERT: A 746 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7369 (m) REVERT: A 1088 GLU cc_start: 0.8147 (tp30) cc_final: 0.7868 (tt0) REVERT: B 29 TYR cc_start: 0.6929 (m-80) cc_final: 0.6627 (m-80) REVERT: B 62 ASN cc_start: 0.6850 (t0) cc_final: 0.6608 (m110) REVERT: B 86 ASN cc_start: 0.7893 (m-40) cc_final: 0.7642 (m110) REVERT: B 218 SER cc_start: 0.8794 (m) cc_final: 0.8225 (p) REVERT: B 528 ASN cc_start: 0.8305 (t0) cc_final: 0.7769 (m110) REVERT: B 543 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8108 (p) REVERT: B 552 ASN cc_start: 0.7407 (p0) cc_final: 0.6729 (m-40) REVERT: B 560 GLN cc_start: 0.7533 (mm110) cc_final: 0.7097 (mm-40) REVERT: B 567 ASP cc_start: 0.8237 (m-30) cc_final: 0.7163 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7590 (tt0) cc_final: 0.6934 (mt-10) REVERT: B 729 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8380 (mttp) REVERT: B 746 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7330 (m) REVERT: B 1088 GLU cc_start: 0.8178 (tp30) cc_final: 0.7877 (tt0) REVERT: B 1109 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: C 117 LEU cc_start: 0.7193 (tp) cc_final: 0.6968 (tp) REVERT: C 218 SER cc_start: 0.8685 (m) cc_final: 0.8055 (p) REVERT: C 543 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 560 GLN cc_start: 0.7639 (mm110) cc_final: 0.7248 (mm-40) REVERT: C 579 GLU cc_start: 0.7613 (tt0) cc_final: 0.6788 (mt-10) REVERT: C 729 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: C 746 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7459 (m) REVERT: C 973 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7953 (mp) REVERT: C 1088 GLU cc_start: 0.8169 (tp30) cc_final: 0.7926 (tp30) REVERT: C 1134 TYR cc_start: 0.8309 (m-80) cc_final: 0.8029 (m-80) outliers start: 90 outliers final: 36 residues processed: 250 average time/residue: 0.5353 time to fit residues: 163.7792 Evaluate side-chains 205 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 279 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 291 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 130 optimal weight: 0.0470 chunk 266 optimal weight: 20.0000 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 318 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS B 183 ASN B 318 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 311 GLN C 318 GLN C 528 ASN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.209017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137086 restraints weight = 52874.238| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.85 r_work: 0.3278 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28428 Z= 0.141 Angle : 0.629 22.477 38805 Z= 0.301 Chirality : 0.047 0.805 4521 Planarity : 0.004 0.052 4881 Dihedral : 6.050 57.613 5035 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.57 % Allowed : 20.73 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3387 helix: 2.09 (0.18), residues: 774 sheet: 0.14 (0.17), residues: 759 loop : -0.70 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 234 TYR 0.017 0.001 TYR A1063 PHE 0.014 0.001 PHE A1117 TRP 0.015 0.001 TRP C 629 HIS 0.002 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00329 (28320) covalent geometry : angle 0.56319 (38523) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.66965 ( 84) hydrogen bonds : bond 0.04061 ( 1184) hydrogen bonds : angle 5.23735 ( 3309) link_BETA1-4 : bond 0.00224 ( 18) link_BETA1-4 : angle 1.20862 ( 54) link_BETA1-6 : bond 0.00367 ( 3) link_BETA1-6 : angle 1.24518 ( 9) link_NAG-ASN : bond 0.01024 ( 45) link_NAG-ASN : angle 4.57406 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7375 (mtp180) REVERT: A 218 SER cc_start: 0.8719 (m) cc_final: 0.8175 (p) REVERT: A 528 ASN cc_start: 0.8317 (t0) cc_final: 0.7679 (m110) REVERT: A 560 GLN cc_start: 0.7408 (mm110) cc_final: 0.7095 (mm-40) REVERT: A 579 GLU cc_start: 0.7476 (tt0) cc_final: 0.6675 (mt-10) REVERT: A 729 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8405 (mttp) REVERT: A 746 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7231 (m) REVERT: A 1088 GLU cc_start: 0.8095 (tp30) cc_final: 0.7794 (tt0) REVERT: A 1134 TYR cc_start: 0.8333 (m-80) cc_final: 0.8019 (m-80) REVERT: B 29 TYR cc_start: 0.6902 (m-80) cc_final: 0.6395 (m-80) REVERT: B 93 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.6833 (t) REVERT: B 218 SER cc_start: 0.8778 (m) cc_final: 0.8237 (p) REVERT: B 234 ARG cc_start: 0.7403 (mtp85) cc_final: 0.6888 (ttp-110) REVERT: B 528 ASN cc_start: 0.8301 (t0) cc_final: 0.7759 (m110) REVERT: B 552 ASN cc_start: 0.7453 (p0) cc_final: 0.6751 (m110) REVERT: B 560 GLN cc_start: 0.7543 (mm110) cc_final: 0.7094 (mm-40) REVERT: B 567 ASP cc_start: 0.8160 (m-30) cc_final: 0.7036 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7555 (tt0) cc_final: 0.6881 (mt-10) REVERT: B 729 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8322 (mttt) REVERT: B 746 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7247 (m) REVERT: B 1088 GLU cc_start: 0.8127 (tp30) cc_final: 0.7827 (tt0) REVERT: B 1109 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: C 117 LEU cc_start: 0.7148 (tp) cc_final: 0.6946 (tp) REVERT: C 218 SER cc_start: 0.8663 (m) cc_final: 0.8060 (p) REVERT: C 234 ARG cc_start: 0.7451 (mtp85) cc_final: 0.6963 (ttp-110) REVERT: C 560 GLN cc_start: 0.7573 (mm110) cc_final: 0.7170 (mm-40) REVERT: C 579 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6831 (mt-10) REVERT: C 729 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8356 (mtmt) REVERT: C 746 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7353 (m) REVERT: C 973 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7920 (mp) REVERT: C 1088 GLU cc_start: 0.8132 (tp30) cc_final: 0.7881 (tp30) REVERT: C 1134 TYR cc_start: 0.8286 (m-80) cc_final: 0.8011 (m-80) outliers start: 58 outliers final: 27 residues processed: 217 average time/residue: 0.5551 time to fit residues: 144.0025 Evaluate side-chains 192 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 930 ILE Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 272 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 205 HIS A 318 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 311 GLN C 318 GLN C 528 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.205059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130710 restraints weight = 48699.634| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.96 r_work: 0.3078 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 28428 Z= 0.267 Angle : 0.692 13.521 38805 Z= 0.344 Chirality : 0.050 0.664 4521 Planarity : 0.004 0.056 4881 Dihedral : 6.464 58.146 5032 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.01 % Allowed : 20.63 % Favored : 76.36 % 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: -0.08 (0.14), residues: 3387 helix: 1.78 (0.18), residues: 774 sheet: -0.04 (0.17), residues: 762 loop : -0.86 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 234 TYR 0.019 0.002 TYR A1063 PHE 0.018 0.002 PHE B 66 TRP 0.015 0.002 TRP B 629 HIS 0.005 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00661 (28320) covalent geometry : angle 0.64759 (38523) SS BOND : bond 0.00523 ( 42) SS BOND : angle 2.25644 ( 84) hydrogen bonds : bond 0.05141 ( 1184) hydrogen bonds : angle 5.42111 ( 3309) link_BETA1-4 : bond 0.00229 ( 18) link_BETA1-4 : angle 1.59966 ( 54) link_BETA1-6 : bond 0.00230 ( 3) link_BETA1-6 : angle 1.51564 ( 9) link_NAG-ASN : bond 0.00859 ( 45) link_NAG-ASN : angle 3.71491 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.975 Fit side-chains REVERT: A 218 SER cc_start: 0.8754 (m) cc_final: 0.8161 (p) REVERT: A 528 ASN cc_start: 0.8332 (t0) cc_final: 0.7678 (m-40) REVERT: A 543 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 560 GLN cc_start: 0.7368 (mm110) cc_final: 0.6982 (mm-40) REVERT: A 579 GLU cc_start: 0.7525 (tt0) cc_final: 0.6699 (mt-10) REVERT: A 729 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8391 (mtmt) REVERT: A 746 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7220 (m) REVERT: A 1088 GLU cc_start: 0.8155 (tp30) cc_final: 0.7867 (tt0) REVERT: B 29 TYR cc_start: 0.7059 (m-80) cc_final: 0.6746 (m-80) REVERT: B 218 SER cc_start: 0.8772 (m) cc_final: 0.8263 (p) REVERT: B 528 ASN cc_start: 0.8296 (t0) cc_final: 0.7708 (m110) REVERT: B 543 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8125 (p) REVERT: B 560 GLN cc_start: 0.7377 (mm110) cc_final: 0.6861 (mm-40) REVERT: B 567 ASP cc_start: 0.8207 (m-30) cc_final: 0.7096 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7636 (tt0) cc_final: 0.6874 (mt-10) REVERT: B 729 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8215 (mttt) REVERT: B 746 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7177 (m) REVERT: B 1088 GLU cc_start: 0.8168 (tp30) cc_final: 0.7889 (tt0) REVERT: C 218 SER cc_start: 0.8675 (m) cc_final: 0.8080 (p) REVERT: C 543 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 560 GLN cc_start: 0.7424 (mm110) cc_final: 0.6964 (mm-40) REVERT: C 579 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: C 729 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: C 746 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7253 (m) REVERT: C 973 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7880 (mp) REVERT: C 1088 GLU cc_start: 0.8166 (tp30) cc_final: 0.7938 (tp30) REVERT: C 1134 TYR cc_start: 0.8233 (m-80) cc_final: 0.7940 (m-80) outliers start: 72 outliers final: 42 residues processed: 234 average time/residue: 0.5644 time to fit residues: 159.8614 Evaluate side-chains 210 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 222 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 323 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 318 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B1109 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 311 GLN C 528 ASN ** C1155 HIS B ** 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 = 0.4308 r_free = 0.4308 target = 0.207509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129830 restraints weight = 46146.362| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.67 r_work: 0.3119 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28428 Z= 0.143 Angle : 0.621 26.113 38805 Z= 0.303 Chirality : 0.046 0.541 4521 Planarity : 0.004 0.052 4881 Dihedral : 6.466 85.306 5026 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.61 % Allowed : 20.90 % Favored : 76.50 % 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: 3387 helix: 2.16 (0.19), residues: 753 sheet: 0.02 (0.17), residues: 759 loop : -0.85 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 234 TYR 0.017 0.001 TYR A1063 PHE 0.015 0.001 PHE C1117 TRP 0.015 0.001 TRP A 629 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00334 (28320) covalent geometry : angle 0.56762 (38523) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.77453 ( 84) hydrogen bonds : bond 0.04218 ( 1184) hydrogen bonds : angle 5.27075 ( 3309) link_BETA1-4 : bond 0.00174 ( 18) link_BETA1-4 : angle 1.25994 ( 54) link_BETA1-6 : bond 0.00340 ( 3) link_BETA1-6 : angle 1.25496 ( 9) link_NAG-ASN : bond 0.00801 ( 45) link_NAG-ASN : angle 4.04095 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.807 Fit side-chains REVERT: A 29 TYR cc_start: 0.6863 (m-80) cc_final: 0.6610 (m-80) REVERT: A 188 ARG cc_start: 0.7760 (mtp180) cc_final: 0.7480 (mtp180) REVERT: A 218 SER cc_start: 0.8767 (m) cc_final: 0.8225 (p) REVERT: A 528 ASN cc_start: 0.8306 (t0) cc_final: 0.7720 (m-40) REVERT: A 543 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 560 GLN cc_start: 0.7324 (mm110) cc_final: 0.6997 (mm-40) REVERT: A 579 GLU cc_start: 0.7488 (tt0) cc_final: 0.6725 (mt-10) REVERT: A 729 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: A 746 SER cc_start: 0.8053 (OUTLIER) cc_final: 0.7461 (m) REVERT: A 1088 GLU cc_start: 0.8146 (tp30) cc_final: 0.7856 (tt0) REVERT: B 218 SER cc_start: 0.8804 (m) cc_final: 0.8373 (p) REVERT: B 234 ARG cc_start: 0.7629 (mtp85) cc_final: 0.6951 (ttp-110) REVERT: B 528 ASN cc_start: 0.8306 (t0) cc_final: 0.7769 (m110) REVERT: B 543 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 560 GLN cc_start: 0.7426 (mm110) cc_final: 0.6971 (mm-40) REVERT: B 567 ASP cc_start: 0.8227 (m-30) cc_final: 0.7086 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7603 (tt0) cc_final: 0.6956 (mt-10) REVERT: B 729 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8468 (mtmm) REVERT: B 746 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7449 (m) REVERT: B 1088 GLU cc_start: 0.8141 (tp30) cc_final: 0.7843 (tt0) REVERT: C 93 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6919 (t) REVERT: C 218 SER cc_start: 0.8702 (m) cc_final: 0.8144 (p) REVERT: C 234 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7043 (ttm110) REVERT: C 543 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 560 GLN cc_start: 0.7449 (mm110) cc_final: 0.7094 (mm-40) REVERT: C 579 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: C 729 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: C 746 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7531 (m) REVERT: C 1088 GLU cc_start: 0.8143 (tp30) cc_final: 0.7899 (tp30) REVERT: C 1134 TYR cc_start: 0.8379 (m-80) cc_final: 0.8126 (m-80) outliers start: 60 outliers final: 33 residues processed: 217 average time/residue: 0.5568 time to fit residues: 144.7804 Evaluate side-chains 197 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1109 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 174 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 236 optimal weight: 30.0000 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 30.0000 chunk 288 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 318 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 318 GLN C 528 ASN ** C1155 HIS B ** 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 = 0.4318 r_free = 0.4318 target = 0.208566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137045 restraints weight = 53908.841| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.83 r_work: 0.3286 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28428 Z= 0.121 Angle : 0.591 18.861 38805 Z= 0.289 Chirality : 0.045 0.477 4521 Planarity : 0.004 0.052 4881 Dihedral : 6.169 60.033 5026 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.37 % Allowed : 21.13 % Favored : 76.50 % 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: 0.19 (0.14), residues: 3387 helix: 2.34 (0.19), residues: 753 sheet: 0.12 (0.18), residues: 750 loop : -0.80 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 234 TYR 0.017 0.001 TYR A1063 PHE 0.015 0.001 PHE C1117 TRP 0.014 0.001 TRP A 629 HIS 0.002 0.000 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00276 (28320) covalent geometry : angle 0.54553 (38523) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.61508 ( 84) hydrogen bonds : bond 0.03900 ( 1184) hydrogen bonds : angle 5.15804 ( 3309) link_BETA1-4 : bond 0.00238 ( 18) link_BETA1-4 : angle 1.16202 ( 54) link_BETA1-6 : bond 0.00363 ( 3) link_BETA1-6 : angle 1.20932 ( 9) link_NAG-ASN : bond 0.00729 ( 45) link_NAG-ASN : angle 3.63072 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.931 Fit side-chains REVERT: A 29 TYR cc_start: 0.6922 (m-80) cc_final: 0.6650 (m-80) REVERT: A 120 ASN cc_start: 0.5802 (t0) cc_final: 0.5461 (t0) REVERT: A 188 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7345 (mtp180) REVERT: A 218 SER cc_start: 0.8762 (m) cc_final: 0.8182 (p) REVERT: A 528 ASN cc_start: 0.8269 (t0) cc_final: 0.7665 (m-40) REVERT: A 543 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 560 GLN cc_start: 0.7312 (mm110) cc_final: 0.6968 (mm-40) REVERT: A 579 GLU cc_start: 0.7539 (tt0) cc_final: 0.6762 (mt-10) REVERT: A 729 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8564 (mtmm) REVERT: A 746 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7348 (m) REVERT: A 1088 GLU cc_start: 0.8093 (tp30) cc_final: 0.7788 (tt0) REVERT: A 1134 TYR cc_start: 0.8377 (m-80) cc_final: 0.8060 (m-80) REVERT: B 218 SER cc_start: 0.8806 (m) cc_final: 0.8355 (p) REVERT: B 234 ARG cc_start: 0.7509 (mtp85) cc_final: 0.6835 (ttp-110) REVERT: B 528 ASN cc_start: 0.8267 (t0) cc_final: 0.7705 (m110) REVERT: B 560 GLN cc_start: 0.7428 (mm110) cc_final: 0.6970 (mm-40) REVERT: B 567 ASP cc_start: 0.8161 (m-30) cc_final: 0.7063 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7636 (tt0) cc_final: 0.6985 (mt-10) REVERT: B 729 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: B 746 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7358 (m) REVERT: B 1088 GLU cc_start: 0.8124 (tp30) cc_final: 0.7831 (tt0) REVERT: C 218 SER cc_start: 0.8694 (m) cc_final: 0.8119 (p) REVERT: C 234 ARG cc_start: 0.7539 (mtp85) cc_final: 0.6964 (ttm110) REVERT: C 528 ASN cc_start: 0.8269 (t0) cc_final: 0.7741 (m110) REVERT: C 543 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 560 GLN cc_start: 0.7489 (mm110) cc_final: 0.7113 (mm-40) REVERT: C 579 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: C 729 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: C 746 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7432 (m) REVERT: C 772 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7717 (tttm) REVERT: C 973 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7924 (mp) REVERT: C 1088 GLU cc_start: 0.8129 (tp30) cc_final: 0.7889 (tp30) REVERT: C 1134 TYR cc_start: 0.8303 (m-80) cc_final: 0.8057 (m-80) outliers start: 53 outliers final: 27 residues processed: 212 average time/residue: 0.5230 time to fit residues: 134.4490 Evaluate side-chains 195 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 278 optimal weight: 0.0170 chunk 31 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 141 optimal weight: 0.2980 chunk 228 optimal weight: 9.9990 chunk 43 optimal weight: 40.0000 chunk 302 optimal weight: 9.9990 chunk 4 optimal weight: 0.0870 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.207198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134540 restraints weight = 51544.143| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.93 r_work: 0.3258 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28428 Z= 0.160 Angle : 0.613 17.022 38805 Z= 0.300 Chirality : 0.045 0.275 4521 Planarity : 0.004 0.052 4881 Dihedral : 6.416 92.115 5024 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.04 % Allowed : 21.53 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3387 helix: 2.27 (0.18), residues: 753 sheet: 0.14 (0.18), residues: 753 loop : -0.82 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 234 TYR 0.018 0.001 TYR A1063 PHE 0.015 0.001 PHE A1117 TRP 0.016 0.001 TRP A 629 HIS 0.003 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00387 (28320) covalent geometry : angle 0.57181 (38523) SS BOND : bond 0.00383 ( 42) SS BOND : angle 1.95655 ( 84) hydrogen bonds : bond 0.04224 ( 1184) hydrogen bonds : angle 5.19899 ( 3309) link_BETA1-4 : bond 0.00207 ( 18) link_BETA1-4 : angle 1.24299 ( 54) link_BETA1-6 : bond 0.00324 ( 3) link_BETA1-6 : angle 1.29211 ( 9) link_NAG-ASN : bond 0.00709 ( 45) link_NAG-ASN : angle 3.38925 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 1.055 Fit side-chains REVERT: A 29 TYR cc_start: 0.6879 (m-80) cc_final: 0.6477 (m-80) REVERT: A 120 ASN cc_start: 0.5947 (t0) cc_final: 0.5603 (t0) REVERT: A 188 ARG cc_start: 0.7665 (mtp180) cc_final: 0.7357 (mtp180) REVERT: A 218 SER cc_start: 0.8773 (m) cc_final: 0.8198 (p) REVERT: A 528 ASN cc_start: 0.8257 (t0) cc_final: 0.7653 (m-40) REVERT: A 543 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 560 GLN cc_start: 0.7354 (mm110) cc_final: 0.7004 (mm-40) REVERT: A 579 GLU cc_start: 0.7554 (tt0) cc_final: 0.6778 (mt-10) REVERT: A 729 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: A 746 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7322 (m) REVERT: A 1088 GLU cc_start: 0.8090 (tp30) cc_final: 0.7783 (tt0) REVERT: B 218 SER cc_start: 0.8806 (m) cc_final: 0.8359 (p) REVERT: B 234 ARG cc_start: 0.7545 (mtp85) cc_final: 0.6818 (ttp-110) REVERT: B 528 ASN cc_start: 0.8271 (t0) cc_final: 0.7706 (m110) REVERT: B 543 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 560 GLN cc_start: 0.7426 (mm110) cc_final: 0.6924 (mm-40) REVERT: B 567 ASP cc_start: 0.8169 (m-30) cc_final: 0.7046 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7646 (tt0) cc_final: 0.6988 (mt-10) REVERT: B 729 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8302 (mttt) REVERT: B 746 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7345 (m) REVERT: B 1088 GLU cc_start: 0.8134 (tp30) cc_final: 0.7836 (tt0) REVERT: C 218 SER cc_start: 0.8730 (m) cc_final: 0.8152 (p) REVERT: C 234 ARG cc_start: 0.7554 (mtp85) cc_final: 0.6932 (ttm110) REVERT: C 543 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8119 (p) REVERT: C 560 GLN cc_start: 0.7499 (mm110) cc_final: 0.7113 (mm-40) REVERT: C 579 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6881 (mt-10) REVERT: C 729 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8293 (mtmt) REVERT: C 746 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7425 (m) REVERT: C 973 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7922 (mp) REVERT: C 1088 GLU cc_start: 0.8122 (tp30) cc_final: 0.7877 (tp30) REVERT: C 1134 TYR cc_start: 0.8319 (m-80) cc_final: 0.8063 (m-80) outliers start: 43 outliers final: 30 residues processed: 201 average time/residue: 0.5618 time to fit residues: 136.2191 Evaluate side-chains 196 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 528 ASN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.205853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124523 restraints weight = 44377.742| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.16 r_work: 0.3003 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 28428 Z= 0.198 Angle : 0.648 16.277 38805 Z= 0.318 Chirality : 0.047 0.283 4521 Planarity : 0.004 0.053 4881 Dihedral : 6.212 67.621 5023 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.27 % Allowed : 21.23 % Favored : 76.50 % 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: 0.03 (0.14), residues: 3387 helix: 1.96 (0.18), residues: 774 sheet: 0.08 (0.18), residues: 753 loop : -0.85 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 234 TYR 0.018 0.001 TYR A1063 PHE 0.017 0.002 PHE B 66 TRP 0.014 0.002 TRP A 629 HIS 0.004 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00487 (28320) covalent geometry : angle 0.60075 (38523) SS BOND : bond 0.00438 ( 42) SS BOND : angle 2.15413 ( 84) hydrogen bonds : bond 0.04577 ( 1184) hydrogen bonds : angle 5.28104 ( 3309) link_BETA1-4 : bond 0.00233 ( 18) link_BETA1-4 : angle 1.35800 ( 54) link_BETA1-6 : bond 0.00215 ( 3) link_BETA1-6 : angle 1.32223 ( 9) link_NAG-ASN : bond 0.00781 ( 45) link_NAG-ASN : angle 3.71674 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.019 Fit side-chains REVERT: A 120 ASN cc_start: 0.6045 (t0) cc_final: 0.5682 (t0) REVERT: A 188 ARG cc_start: 0.7578 (mtp180) cc_final: 0.7262 (mtp180) REVERT: A 218 SER cc_start: 0.8770 (m) cc_final: 0.8177 (p) REVERT: A 528 ASN cc_start: 0.8305 (t0) cc_final: 0.7641 (m-40) REVERT: A 543 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 560 GLN cc_start: 0.7324 (mm110) cc_final: 0.6951 (mm-40) REVERT: A 579 GLU cc_start: 0.7577 (tt0) cc_final: 0.6763 (mt-10) REVERT: A 729 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8466 (mtmt) REVERT: A 746 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7272 (m) REVERT: A 1088 GLU cc_start: 0.8196 (tp30) cc_final: 0.7886 (tt0) REVERT: B 218 SER cc_start: 0.8779 (m) cc_final: 0.8332 (p) REVERT: B 528 ASN cc_start: 0.8291 (t0) cc_final: 0.7661 (m110) REVERT: B 543 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 567 ASP cc_start: 0.8134 (m-30) cc_final: 0.7011 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7701 (tt0) cc_final: 0.6948 (mt-10) REVERT: B 729 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8340 (mtmt) REVERT: B 746 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7226 (m) REVERT: B 1088 GLU cc_start: 0.8225 (tp30) cc_final: 0.7929 (tt0) REVERT: C 93 SER cc_start: 0.7144 (OUTLIER) cc_final: 0.6809 (t) REVERT: C 218 SER cc_start: 0.8719 (m) cc_final: 0.8135 (p) REVERT: C 560 GLN cc_start: 0.7444 (mm110) cc_final: 0.6940 (mm-40) REVERT: C 579 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: C 729 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8464 (mtmt) REVERT: C 746 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7319 (m) REVERT: C 973 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 1088 GLU cc_start: 0.8222 (tp30) cc_final: 0.7991 (tp30) outliers start: 50 outliers final: 32 residues processed: 213 average time/residue: 0.5380 time to fit residues: 138.8735 Evaluate side-chains 203 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 220 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 528 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130243 restraints weight = 51888.430| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.04 r_work: 0.3215 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 28428 Z= 0.258 Angle : 0.730 29.080 38805 Z= 0.352 Chirality : 0.049 0.391 4521 Planarity : 0.004 0.054 4881 Dihedral : 7.005 123.170 5023 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.14 % Allowed : 21.53 % Favored : 76.33 % 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: -0.18 (0.14), residues: 3387 helix: 1.74 (0.18), residues: 774 sheet: -0.04 (0.18), residues: 756 loop : -0.97 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 234 TYR 0.019 0.002 TYR A1063 PHE 0.026 0.002 PHE B 60 TRP 0.015 0.002 TRP A 255 HIS 0.006 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00638 (28320) covalent geometry : angle 0.66487 (38523) SS BOND : bond 0.00522 ( 42) SS BOND : angle 2.37545 ( 84) hydrogen bonds : bond 0.05040 ( 1184) hydrogen bonds : angle 5.41490 ( 3309) link_BETA1-4 : bond 0.00260 ( 18) link_BETA1-4 : angle 1.53307 ( 54) link_BETA1-6 : bond 0.00152 ( 3) link_BETA1-6 : angle 1.42707 ( 9) link_NAG-ASN : bond 0.00870 ( 45) link_NAG-ASN : angle 4.74909 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 120 ASN cc_start: 0.6217 (t0) cc_final: 0.5860 (t0) REVERT: A 218 SER cc_start: 0.8808 (m) cc_final: 0.8256 (p) REVERT: A 528 ASN cc_start: 0.8317 (t0) cc_final: 0.7995 (t0) REVERT: A 543 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 560 GLN cc_start: 0.7281 (mm110) cc_final: 0.6966 (mm-40) REVERT: A 579 GLU cc_start: 0.7558 (tt0) cc_final: 0.6766 (mt-10) REVERT: A 729 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8491 (mtmt) REVERT: A 746 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7482 (m) REVERT: A 1088 GLU cc_start: 0.8156 (tp30) cc_final: 0.7855 (tt0) REVERT: B 86 ASN cc_start: 0.7808 (m-40) cc_final: 0.7583 (m110) REVERT: B 120 ASN cc_start: 0.6016 (t0) cc_final: 0.5667 (t0) REVERT: B 218 SER cc_start: 0.8816 (m) cc_final: 0.8422 (p) REVERT: B 528 ASN cc_start: 0.8321 (t0) cc_final: 0.8062 (t0) REVERT: B 567 ASP cc_start: 0.8231 (m-30) cc_final: 0.7145 (OUTLIER) REVERT: B 579 GLU cc_start: 0.7636 (tt0) cc_final: 0.6934 (mt-10) REVERT: B 722 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9227 (mt) REVERT: B 729 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8273 (mttt) REVERT: B 746 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7376 (m) REVERT: B 1088 GLU cc_start: 0.8123 (tp30) cc_final: 0.7815 (tt0) REVERT: C 93 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6922 (t) REVERT: C 218 SER cc_start: 0.8791 (m) cc_final: 0.8254 (p) REVERT: C 560 GLN cc_start: 0.7428 (mm110) cc_final: 0.7004 (mm-40) REVERT: C 579 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: C 729 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8483 (mtmt) REVERT: C 746 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7435 (m) REVERT: C 973 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 1088 GLU cc_start: 0.8141 (tp30) cc_final: 0.7900 (tp30) outliers start: 46 outliers final: 31 residues processed: 210 average time/residue: 0.5113 time to fit residues: 130.9589 Evaluate side-chains 209 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 579 GLU Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 103 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 300 optimal weight: 0.0020 chunk 189 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 297 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 overall best weight: 1.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 311 GLN C 528 ASN ** C1155 HIS B ** 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 = 0.4310 r_free = 0.4310 target = 0.207581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135563 restraints weight = 59960.073| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.26 r_work: 0.3262 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28428 Z= 0.129 Angle : 0.617 21.627 38805 Z= 0.300 Chirality : 0.045 0.398 4521 Planarity : 0.004 0.051 4881 Dihedral : 6.687 125.573 5023 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.84 % Allowed : 21.83 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3387 helix: 2.06 (0.18), residues: 771 sheet: 0.01 (0.18), residues: 726 loop : -0.87 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 234 TYR 0.017 0.001 TYR A1063 PHE 0.015 0.001 PHE A 235 TRP 0.015 0.001 TRP A 629 HIS 0.002 0.000 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00290 (28320) covalent geometry : angle 0.56099 (38523) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.74297 ( 84) hydrogen bonds : bond 0.03978 ( 1184) hydrogen bonds : angle 5.22679 ( 3309) link_BETA1-4 : bond 0.00258 ( 18) link_BETA1-4 : angle 1.18649 ( 54) link_BETA1-6 : bond 0.00410 ( 3) link_BETA1-6 : angle 1.16338 ( 9) link_NAG-ASN : bond 0.01120 ( 45) link_NAG-ASN : angle 4.12590 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13446.35 seconds wall clock time: 228 minutes 48.69 seconds (13728.69 seconds total)