Starting phenix.real_space_refine on Fri Mar 6 05:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbm_27290/03_2026/8dbm_27290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbm_27290/03_2026/8dbm_27290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbm_27290/03_2026/8dbm_27290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbm_27290/03_2026/8dbm_27290.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbm_27290/03_2026/8dbm_27290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbm_27290/03_2026/8dbm_27290.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.390 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 24 5.21 5 S 204 5.16 5 C 17844 2.51 5 N 4980 2.21 5 O 5616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28716 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "H" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 636 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 624 not shown) Time building chain proxies: 5.38, per 1000 atoms: 0.19 Number of scatterers: 28716 At special positions: 0 Unit cell: (128.018, 138.598, 140.714, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 48 15.00 Mg 24 11.99 O 5616 8.00 N 4980 7.00 C 17844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 43.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 removed outlier: 3.524A pdb=" N PHE B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.667A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 removed outlier: 3.524A pdb=" N PHE D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 removed outlier: 3.526A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.524A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 283 removed outlier: 3.667A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 315 Processing helix chain 'G' and resid 12 through 23 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE G 138 " --> pdb=" O GLN G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 Processing helix chain 'G' and resid 171 through 173 No H-bonds generated for 'chain 'G' and resid 171 through 173' Processing helix chain 'G' and resid 174 through 186 Processing helix chain 'G' and resid 226 through 239 Processing helix chain 'G' and resid 256 through 264 Processing helix chain 'G' and resid 277 through 283 removed outlier: 3.667A pdb=" N HIS G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 306 Processing helix chain 'G' and resid 309 through 315 Processing helix chain 'H' and resid 12 through 23 Processing helix chain 'H' and resid 62 through 80 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE H 138 " --> pdb=" O GLN H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 159 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 174 through 186 Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 256 through 264 Processing helix chain 'H' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 306 Processing helix chain 'H' and resid 309 through 315 Processing helix chain 'I' and resid 12 through 23 Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE I 138 " --> pdb=" O GLN I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 159 Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 174 through 186 Processing helix chain 'I' and resid 226 through 239 Processing helix chain 'I' and resid 256 through 264 Processing helix chain 'I' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS I 283 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 306 Processing helix chain 'I' and resid 309 through 315 Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 62 through 80 Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 174 through 186 Processing helix chain 'J' and resid 226 through 239 Processing helix chain 'J' and resid 256 through 264 Processing helix chain 'J' and resid 277 through 283 removed outlier: 3.667A pdb=" N HIS J 283 " --> pdb=" O ASP J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 306 Processing helix chain 'J' and resid 309 through 315 Processing helix chain 'K' and resid 12 through 23 Processing helix chain 'K' and resid 62 through 80 Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 159 Processing helix chain 'K' and resid 171 through 173 No H-bonds generated for 'chain 'K' and resid 171 through 173' Processing helix chain 'K' and resid 174 through 186 Processing helix chain 'K' and resid 226 through 239 Processing helix chain 'K' and resid 256 through 264 Processing helix chain 'K' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS K 283 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 306 Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'L' and resid 12 through 23 Processing helix chain 'L' and resid 62 through 80 Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 131 through 138 removed outlier: 3.524A pdb=" N PHE L 138 " --> pdb=" O GLN L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 159 Processing helix chain 'L' and resid 171 through 173 No H-bonds generated for 'chain 'L' and resid 171 through 173' Processing helix chain 'L' and resid 174 through 186 Processing helix chain 'L' and resid 226 through 239 Processing helix chain 'L' and resid 256 through 264 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS L 283 " --> pdb=" O ASP L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 306 Processing helix chain 'L' and resid 309 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.776A pdb=" N SER A 169 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 249 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 244 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL A 270 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 246 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A 272 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 248 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.776A pdb=" N SER B 169 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 249 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 244 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 270 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 246 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 272 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 248 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER C 169 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 249 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 244 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL C 270 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 246 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR C 272 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU C 248 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER D 169 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR D 249 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 244 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL D 270 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 246 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR D 272 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU D 248 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 3.776A pdb=" N SER E 169 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 249 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL E 244 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL E 270 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA E 246 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR E 272 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU E 248 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER F 169 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR F 249 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL F 244 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL F 270 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 246 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR F 272 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 248 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS G 5 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL G 56 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE G 7 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL G 53 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL G 88 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE G 55 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS G 123 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET G 127 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE G 124 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU G 145 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G 126 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 34 Processing sheet with id=AC3, first strand: chain 'G' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER G 169 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 249 " --> pdb=" O ASP G 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET G 222 " --> pdb=" O THR G 249 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY G 251 " --> pdb=" O MET G 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL G 244 " --> pdb=" O ALA G 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL G 270 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA G 246 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR G 272 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU G 248 " --> pdb=" O THR G 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL G 269 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE G 290 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 271 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS H 5 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE H 7 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL H 88 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE H 55 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS H 123 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET H 127 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU H 145 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 30 through 34 Processing sheet with id=AC6, first strand: chain 'H' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER H 169 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR H 249 " --> pdb=" O ASP H 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET H 222 " --> pdb=" O THR H 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY H 251 " --> pdb=" O MET H 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL H 244 " --> pdb=" O ALA H 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL H 270 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 246 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR H 272 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU H 248 " --> pdb=" O THR H 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL H 269 " --> pdb=" O GLN H 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE H 290 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 271 " --> pdb=" O ILE H 290 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS I 5 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL I 56 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE I 7 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL I 53 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL I 88 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE I 55 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS I 123 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET I 127 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE I 124 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU I 145 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR I 126 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 30 through 34 Processing sheet with id=AC9, first strand: chain 'I' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER I 169 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR I 249 " --> pdb=" O ASP I 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET I 222 " --> pdb=" O THR I 249 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY I 251 " --> pdb=" O MET I 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL I 244 " --> pdb=" O ALA I 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL I 270 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA I 246 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR I 272 " --> pdb=" O ALA I 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU I 248 " --> pdb=" O THR I 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL I 269 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE I 290 " --> pdb=" O VAL I 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 271 " --> pdb=" O ILE I 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS J 5 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL J 56 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE J 7 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL J 53 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL J 88 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE J 55 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS J 123 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET J 127 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE J 124 " --> pdb=" O ASP J 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU J 145 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR J 126 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 30 through 34 Processing sheet with id=AD3, first strand: chain 'J' and resid 205 through 208 removed outlier: 3.774A pdb=" N SER J 169 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR J 249 " --> pdb=" O ASP J 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET J 222 " --> pdb=" O THR J 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY J 251 " --> pdb=" O MET J 222 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL J 244 " --> pdb=" O ALA J 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL J 270 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA J 246 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR J 272 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU J 248 " --> pdb=" O THR J 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL J 269 " --> pdb=" O GLN J 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE J 290 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL J 271 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS K 5 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL K 56 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE K 7 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL K 53 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL K 88 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE K 55 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS K 123 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET K 127 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE K 124 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU K 145 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR K 126 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 34 Processing sheet with id=AD6, first strand: chain 'K' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER K 169 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR K 249 " --> pdb=" O ASP K 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET K 222 " --> pdb=" O THR K 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY K 251 " --> pdb=" O MET K 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL K 244 " --> pdb=" O ALA K 268 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL K 270 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA K 246 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR K 272 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU K 248 " --> pdb=" O THR K 272 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL K 269 " --> pdb=" O GLN K 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE K 290 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL K 271 " --> pdb=" O ILE K 290 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS L 5 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL L 56 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE L 7 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL L 53 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL L 88 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE L 55 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS L 123 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET L 127 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE L 124 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU L 145 " --> pdb=" O ILE L 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR L 126 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 30 through 34 Processing sheet with id=AD9, first strand: chain 'L' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER L 169 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR L 249 " --> pdb=" O ASP L 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET L 222 " --> pdb=" O THR L 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY L 251 " --> pdb=" O MET L 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL L 244 " --> pdb=" O ALA L 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL L 270 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA L 246 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR L 272 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU L 248 " --> pdb=" O THR L 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL L 269 " --> pdb=" O GLN L 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE L 290 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL L 271 " --> pdb=" O ILE L 290 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3600 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: 5.26 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9550 1.34 - 1.46: 4209 1.46 - 1.57: 14969 1.57 - 1.69: 48 1.69 - 1.81: 300 Bond restraints: 29076 Sorted by residual: bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP C 401 " pdb=" O4 PRP C 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP H 401 " pdb=" O4 PRP H 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP G 401 " pdb=" O4 PRP G 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP I 401 " pdb=" O4 PRP I 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 29071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 38205 1.96 - 3.93: 927 3.93 - 5.89: 182 5.89 - 7.85: 64 7.85 - 9.81: 18 Bond angle restraints: 39396 Sorted by residual: angle pdb=" C THR C 272 " pdb=" CA THR C 272 " pdb=" CB THR C 272 " ideal model delta sigma weight residual 109.51 117.40 -7.89 1.71e+00 3.42e-01 2.13e+01 angle pdb=" C THR H 272 " pdb=" CA THR H 272 " pdb=" CB THR H 272 " ideal model delta sigma weight residual 109.51 117.39 -7.88 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR G 272 " pdb=" CA THR G 272 " pdb=" CB THR G 272 " ideal model delta sigma weight residual 109.51 117.38 -7.87 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR I 272 " pdb=" CA THR I 272 " pdb=" CB THR I 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR F 272 " pdb=" CA THR F 272 " pdb=" CB THR F 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 ... (remaining 39391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 16031 17.71 - 35.42: 1315 35.42 - 53.12: 414 53.12 - 70.83: 120 70.83 - 88.54: 72 Dihedral angle restraints: 17952 sinusoidal: 7200 harmonic: 10752 Sorted by residual: dihedral pdb=" CA GLU K 62 " pdb=" C GLU K 62 " pdb=" N ILE K 63 " pdb=" CA ILE K 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 17949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2677 0.041 - 0.083: 1314 0.083 - 0.124: 526 0.124 - 0.165: 91 0.165 - 0.206: 60 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CA THR J 272 " pdb=" N THR J 272 " pdb=" C THR J 272 " pdb=" CB THR J 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR L 272 " pdb=" N THR L 272 " pdb=" C THR L 272 " pdb=" CB THR L 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4665 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 221 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" CG ASP I 221 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP I 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP I 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 221 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" CG ASP E 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 221 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" CG ASP K 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP K 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 221 " 0.015 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 216 2.49 - 3.09: 20651 3.09 - 3.69: 44890 3.69 - 4.30: 68666 4.30 - 4.90: 111975 Nonbonded interactions: 246398 Sorted by model distance: nonbonded pdb=" O3B PRP K 401 " pdb="MG MG K 403 " model vdw 1.884 2.170 nonbonded pdb=" O3B PRP E 401 " pdb="MG MG E 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP C 401 " pdb="MG MG C 403 " model vdw 1.885 2.170 nonbonded pdb=" O1B PRP F 401 " pdb="MG MG F 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP I 401 " pdb="MG MG I 403 " model vdw 1.886 2.170 ... (remaining 246393 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.01 max=1.00 mean=0.91 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.011 0.236 29076 Z= 0.535 Angle : 0.823 9.813 39396 Z= 0.455 Chirality : 0.057 0.206 4668 Planarity : 0.003 0.025 4992 Dihedral : 16.538 88.539 10944 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 15.27 % Favored : 82.06 % 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 (0.15), residues: 3660 helix: 1.25 (0.14), residues: 1476 sheet: -0.62 (0.17), residues: 1044 loop : -0.54 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 177 TYR 0.027 0.004 TYR C 245 PHE 0.017 0.002 PHE K 138 TRP 0.016 0.003 TRP E 162 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.01102 (29076) covalent geometry : angle 0.82343 (39396) hydrogen bonds : bond 0.15501 ( 1296) hydrogen bonds : angle 5.67951 ( 3600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 831 time to evaluate : 0.856 Fit side-chains REVERT: A 5 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8270 (mmmt) REVERT: A 103 SER cc_start: 0.7538 (m) cc_final: 0.7283 (p) REVERT: A 128 ASP cc_start: 0.8351 (m-30) cc_final: 0.8103 (m-30) REVERT: A 180 SER cc_start: 0.8115 (t) cc_final: 0.7741 (t) REVERT: A 281 MET cc_start: 0.7565 (mtp) cc_final: 0.7350 (mtm) REVERT: B 5 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8124 (mmtt) REVERT: B 14 ASP cc_start: 0.7548 (t0) cc_final: 0.7313 (t70) REVERT: B 152 LEU cc_start: 0.8164 (mt) cc_final: 0.7900 (mt) REVERT: B 158 ASN cc_start: 0.7999 (m-40) cc_final: 0.7355 (m-40) REVERT: B 191 LEU cc_start: 0.7511 (mp) cc_final: 0.6428 (tt) REVERT: B 220 ASP cc_start: 0.8083 (t0) cc_final: 0.7758 (t0) REVERT: C 5 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8184 (mmtp) REVERT: C 46 GLU cc_start: 0.8288 (pt0) cc_final: 0.7942 (pt0) REVERT: C 128 ASP cc_start: 0.8407 (m-30) cc_final: 0.8129 (m-30) REVERT: C 260 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7879 (mtt180) REVERT: C 281 MET cc_start: 0.7366 (mtp) cc_final: 0.7125 (mtm) REVERT: D 69 GLU cc_start: 0.8279 (tt0) cc_final: 0.8077 (tt0) REVERT: D 158 ASN cc_start: 0.8065 (m-40) cc_final: 0.7671 (m110) REVERT: D 191 LEU cc_start: 0.7625 (mp) cc_final: 0.6581 (tt) REVERT: D 261 ILE cc_start: 0.8623 (mt) cc_final: 0.8388 (mm) REVERT: E 14 ASP cc_start: 0.7704 (t0) cc_final: 0.7314 (t70) REVERT: E 46 GLU cc_start: 0.8400 (pt0) cc_final: 0.8090 (pt0) REVERT: E 103 SER cc_start: 0.7473 (m) cc_final: 0.7164 (p) REVERT: E 180 SER cc_start: 0.8147 (t) cc_final: 0.7743 (t) REVERT: E 267 GLU cc_start: 0.7503 (tp30) cc_final: 0.7210 (tp30) REVERT: F 158 ASN cc_start: 0.8005 (m-40) cc_final: 0.7791 (m110) REVERT: F 169 SER cc_start: 0.7771 (t) cc_final: 0.7459 (p) REVERT: F 180 SER cc_start: 0.8470 (t) cc_final: 0.7763 (t) REVERT: F 261 ILE cc_start: 0.8623 (mt) cc_final: 0.8407 (mm) REVERT: F 294 MET cc_start: 0.8556 (pmm) cc_final: 0.8221 (pmm) REVERT: G 158 ASN cc_start: 0.8243 (m-40) cc_final: 0.7876 (m110) REVERT: G 191 LEU cc_start: 0.7627 (mp) cc_final: 0.6583 (tt) REVERT: G 261 ILE cc_start: 0.8620 (mt) cc_final: 0.8410 (mm) REVERT: H 5 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8161 (mmtp) REVERT: H 46 GLU cc_start: 0.8282 (pt0) cc_final: 0.7992 (pt0) REVERT: H 128 ASP cc_start: 0.8414 (m-30) cc_final: 0.8120 (m-30) REVERT: H 260 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7890 (mtt180) REVERT: H 281 MET cc_start: 0.7463 (mtp) cc_final: 0.7216 (mtm) REVERT: I 5 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8158 (mmtt) REVERT: I 52 ASP cc_start: 0.8534 (t0) cc_final: 0.8284 (t0) REVERT: I 158 ASN cc_start: 0.8006 (m-40) cc_final: 0.7260 (m110) REVERT: I 191 LEU cc_start: 0.7516 (mp) cc_final: 0.6416 (tt) REVERT: I 220 ASP cc_start: 0.8134 (t0) cc_final: 0.7790 (t0) REVERT: J 5 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8273 (mmmt) REVERT: J 103 SER cc_start: 0.7579 (m) cc_final: 0.7331 (p) REVERT: J 128 ASP cc_start: 0.8367 (m-30) cc_final: 0.8061 (m-30) REVERT: J 180 SER cc_start: 0.8180 (t) cc_final: 0.7763 (t) REVERT: J 281 MET cc_start: 0.7598 (mtp) cc_final: 0.7343 (mtm) REVERT: K 78 LYS cc_start: 0.8505 (tptm) cc_final: 0.7732 (ttmt) REVERT: K 158 ASN cc_start: 0.8018 (m-40) cc_final: 0.7801 (m110) REVERT: K 169 SER cc_start: 0.7781 (t) cc_final: 0.7459 (p) REVERT: K 191 LEU cc_start: 0.7460 (mp) cc_final: 0.6458 (tt) REVERT: K 217 ILE cc_start: 0.8352 (mt) cc_final: 0.8149 (mm) REVERT: K 261 ILE cc_start: 0.8651 (mt) cc_final: 0.8438 (mm) REVERT: K 294 MET cc_start: 0.8576 (pmm) cc_final: 0.8252 (pmm) REVERT: L 14 ASP cc_start: 0.7720 (t0) cc_final: 0.7324 (t70) REVERT: L 46 GLU cc_start: 0.8408 (pt0) cc_final: 0.8087 (pt0) REVERT: L 103 SER cc_start: 0.7520 (m) cc_final: 0.7218 (p) REVERT: L 180 SER cc_start: 0.8172 (t) cc_final: 0.7774 (t) REVERT: L 267 GLU cc_start: 0.7506 (tp30) cc_final: 0.7225 (tp30) outliers start: 84 outliers final: 38 residues processed: 893 average time/residue: 0.6615 time to fit residues: 687.0312 Evaluate side-chains 638 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 594 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN C 97 GLN D 263 ASN E 97 GLN E 277 GLN F 263 ASN G 263 ASN H 97 GLN J 97 GLN K 263 ASN L 97 GLN L 277 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126043 restraints weight = 26302.289| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.72 r_work: 0.3206 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29076 Z= 0.132 Angle : 0.501 5.988 39396 Z= 0.273 Chirality : 0.047 0.175 4668 Planarity : 0.003 0.022 4992 Dihedral : 8.751 69.004 4318 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.12 % Allowed : 14.22 % Favored : 80.66 % 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: 0.86 (0.14), residues: 3660 helix: 1.98 (0.14), residues: 1404 sheet: -0.48 (0.17), residues: 996 loop : 0.01 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 22 TYR 0.012 0.002 TYR A 311 PHE 0.012 0.001 PHE H 35 TRP 0.011 0.002 TRP D 162 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00293 (29076) covalent geometry : angle 0.50057 (39396) hydrogen bonds : bond 0.04045 ( 1296) hydrogen bonds : angle 4.81587 ( 3600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 650 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8723 (mmmt) REVERT: A 103 SER cc_start: 0.8319 (m) cc_final: 0.7858 (p) REVERT: A 128 ASP cc_start: 0.8892 (m-30) cc_final: 0.8666 (m-30) REVERT: A 180 SER cc_start: 0.7842 (t) cc_final: 0.7451 (t) REVERT: A 248 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 260 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7851 (mtt180) REVERT: A 281 MET cc_start: 0.8747 (mtp) cc_final: 0.8359 (mtm) REVERT: B 14 ASP cc_start: 0.8253 (t0) cc_final: 0.7830 (t70) REVERT: B 52 ASP cc_start: 0.8828 (t0) cc_final: 0.8607 (t0) REVERT: B 191 LEU cc_start: 0.6923 (mp) cc_final: 0.5898 (tt) REVERT: B 220 ASP cc_start: 0.8334 (t0) cc_final: 0.7958 (t0) REVERT: B 288 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: C 5 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8701 (mmmt) REVERT: C 13 GLN cc_start: 0.8480 (tp40) cc_final: 0.8253 (mm-40) REVERT: C 128 ASP cc_start: 0.8922 (m-30) cc_final: 0.8706 (m-30) REVERT: C 176 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6665 (ttmt) REVERT: C 248 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8068 (mt) REVERT: C 260 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7732 (mtm-85) REVERT: C 281 MET cc_start: 0.8648 (mtp) cc_final: 0.8090 (mtm) REVERT: C 288 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 294 MET cc_start: 0.8912 (pmm) cc_final: 0.8622 (pmm) REVERT: D 78 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8332 (ttmt) REVERT: D 97 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: D 158 ASN cc_start: 0.8096 (m-40) cc_final: 0.7595 (m110) REVERT: D 261 ILE cc_start: 0.8390 (mt) cc_final: 0.8107 (mm) REVERT: E 14 ASP cc_start: 0.8417 (t0) cc_final: 0.8009 (t70) REVERT: E 46 GLU cc_start: 0.8968 (pt0) cc_final: 0.8711 (pt0) REVERT: E 103 SER cc_start: 0.8491 (m) cc_final: 0.8049 (p) REVERT: E 180 SER cc_start: 0.7829 (t) cc_final: 0.7503 (t) REVERT: E 267 GLU cc_start: 0.7814 (tp30) cc_final: 0.7406 (tp30) REVERT: E 282 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8240 (mmtp) REVERT: F 97 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: F 180 SER cc_start: 0.8295 (t) cc_final: 0.8070 (t) REVERT: F 259 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8098 (p) REVERT: F 261 ILE cc_start: 0.8523 (mt) cc_final: 0.8260 (mm) REVERT: F 294 MET cc_start: 0.8802 (pmm) cc_final: 0.8425 (pmm) REVERT: G 78 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8331 (ttmt) REVERT: G 96 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8460 (mtm180) REVERT: G 97 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: G 158 ASN cc_start: 0.8111 (m-40) cc_final: 0.7608 (m110) REVERT: G 261 ILE cc_start: 0.8362 (mt) cc_final: 0.8109 (mm) REVERT: H 5 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8678 (mmtp) REVERT: H 13 GLN cc_start: 0.8526 (tp40) cc_final: 0.8274 (mm-40) REVERT: H 128 ASP cc_start: 0.8929 (m-30) cc_final: 0.8719 (m-30) REVERT: H 176 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6676 (ttmt) REVERT: H 260 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7727 (mtm-85) REVERT: H 281 MET cc_start: 0.8684 (mtp) cc_final: 0.8121 (mtm) REVERT: H 288 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: H 294 MET cc_start: 0.8918 (pmm) cc_final: 0.8631 (pmm) REVERT: I 14 ASP cc_start: 0.8223 (t0) cc_final: 0.8004 (t70) REVERT: I 97 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: I 191 LEU cc_start: 0.6904 (mp) cc_final: 0.5901 (tt) REVERT: I 288 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: J 5 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8771 (mmmt) REVERT: J 103 SER cc_start: 0.8299 (m) cc_final: 0.7848 (p) REVERT: J 128 ASP cc_start: 0.8891 (m-30) cc_final: 0.8681 (m-30) REVERT: J 180 SER cc_start: 0.7912 (t) cc_final: 0.7520 (t) REVERT: J 248 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (mt) REVERT: J 260 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7874 (mtt180) REVERT: J 281 MET cc_start: 0.8749 (mtp) cc_final: 0.8364 (mtm) REVERT: K 97 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: K 180 SER cc_start: 0.8262 (t) cc_final: 0.8042 (t) REVERT: K 217 ILE cc_start: 0.8195 (mt) cc_final: 0.7961 (mm) REVERT: K 259 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8092 (p) REVERT: K 261 ILE cc_start: 0.8482 (mt) cc_final: 0.8243 (mm) REVERT: K 294 MET cc_start: 0.8785 (pmm) cc_final: 0.8401 (pmm) REVERT: L 14 ASP cc_start: 0.8444 (t0) cc_final: 0.8039 (t70) REVERT: L 103 SER cc_start: 0.8517 (m) cc_final: 0.8073 (p) REVERT: L 180 SER cc_start: 0.7822 (t) cc_final: 0.7488 (t) REVERT: L 267 GLU cc_start: 0.7821 (tp30) cc_final: 0.7439 (tp30) outliers start: 161 outliers final: 91 residues processed: 759 average time/residue: 0.6800 time to fit residues: 597.0440 Evaluate side-chains 730 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 616 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain I residue 12 HIS Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 300 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 309 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 326 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 130 HIS C 97 GLN D 130 HIS D 263 ASN E 130 HIS F 130 HIS F 263 ASN F 305 ASN G 130 HIS G 263 ASN H 97 GLN J 97 GLN J 130 HIS K 130 HIS K 263 ASN L 130 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.158245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111490 restraints weight = 26458.141| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.61 r_work: 0.3017 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29076 Z= 0.108 Angle : 0.470 7.248 39396 Z= 0.253 Chirality : 0.046 0.170 4668 Planarity : 0.003 0.027 4992 Dihedral : 8.053 59.212 4310 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.64 % Allowed : 15.24 % Favored : 80.12 % 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: 0.97 (0.14), residues: 3660 helix: 2.19 (0.14), residues: 1404 sheet: -0.41 (0.17), residues: 996 loop : -0.11 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 22 TYR 0.012 0.001 TYR E 146 PHE 0.010 0.001 PHE B 35 TRP 0.008 0.002 TRP D 162 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00237 (29076) covalent geometry : angle 0.47037 (39396) hydrogen bonds : bond 0.03587 ( 1296) hydrogen bonds : angle 4.55534 ( 3600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 638 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8254 (mm-40) REVERT: A 103 SER cc_start: 0.8276 (m) cc_final: 0.7859 (p) REVERT: A 132 SER cc_start: 0.8878 (p) cc_final: 0.8635 (t) REVERT: A 180 SER cc_start: 0.7869 (t) cc_final: 0.7517 (t) REVERT: A 248 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 260 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7779 (mtt180) REVERT: A 281 MET cc_start: 0.8772 (mtp) cc_final: 0.8386 (mtm) REVERT: B 14 ASP cc_start: 0.8132 (t0) cc_final: 0.7685 (t70) REVERT: B 52 ASP cc_start: 0.8770 (t0) cc_final: 0.8536 (t0) REVERT: B 79 ILE cc_start: 0.8879 (pt) cc_final: 0.8641 (mm) REVERT: B 191 LEU cc_start: 0.6795 (mp) cc_final: 0.6024 (tt) REVERT: C 115 MET cc_start: 0.9009 (mtp) cc_final: 0.8764 (mtp) REVERT: C 128 ASP cc_start: 0.8814 (m-30) cc_final: 0.8611 (m-30) REVERT: C 260 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7636 (mtm-85) REVERT: C 281 MET cc_start: 0.8637 (mtp) cc_final: 0.8214 (mtm) REVERT: C 294 MET cc_start: 0.8896 (pmm) cc_final: 0.8631 (pmm) REVERT: D 78 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: D 97 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: D 103 SER cc_start: 0.8315 (m) cc_final: 0.8019 (t) REVERT: D 261 ILE cc_start: 0.8384 (mt) cc_final: 0.8132 (mm) REVERT: D 267 GLU cc_start: 0.8178 (tp30) cc_final: 0.7729 (tp30) REVERT: E 14 ASP cc_start: 0.8380 (t0) cc_final: 0.7983 (t70) REVERT: E 46 GLU cc_start: 0.8893 (pt0) cc_final: 0.8626 (pt0) REVERT: E 103 SER cc_start: 0.8532 (m) cc_final: 0.8069 (p) REVERT: E 248 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8165 (mt) REVERT: E 260 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7860 (mtm-85) REVERT: E 267 GLU cc_start: 0.7728 (tp30) cc_final: 0.7301 (tp30) REVERT: E 282 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: F 180 SER cc_start: 0.8268 (t) cc_final: 0.7991 (t) REVERT: F 261 ILE cc_start: 0.8384 (mt) cc_final: 0.8162 (mm) REVERT: F 288 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: F 294 MET cc_start: 0.8739 (pmm) cc_final: 0.8388 (pmm) REVERT: G 68 MET cc_start: 0.8691 (tpp) cc_final: 0.8444 (tpt) REVERT: G 78 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8296 (ttmt) REVERT: G 97 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: G 103 SER cc_start: 0.8309 (m) cc_final: 0.8013 (t) REVERT: G 245 TYR cc_start: 0.8585 (m-80) cc_final: 0.8293 (m-80) REVERT: H 115 MET cc_start: 0.9011 (mtp) cc_final: 0.8769 (mtp) REVERT: H 248 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8054 (mt) REVERT: H 260 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7574 (mtm-85) REVERT: H 281 MET cc_start: 0.8665 (mtp) cc_final: 0.8244 (mtm) REVERT: H 294 MET cc_start: 0.8891 (pmm) cc_final: 0.8625 (pmm) REVERT: I 14 ASP cc_start: 0.8110 (t0) cc_final: 0.7857 (t70) REVERT: I 52 ASP cc_start: 0.8755 (t0) cc_final: 0.8538 (t0) REVERT: I 79 ILE cc_start: 0.8886 (pt) cc_final: 0.8634 (mm) REVERT: I 191 LEU cc_start: 0.6752 (mp) cc_final: 0.6016 (tt) REVERT: I 288 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: J 103 SER cc_start: 0.8242 (m) cc_final: 0.7823 (p) REVERT: J 132 SER cc_start: 0.8879 (p) cc_final: 0.8631 (t) REVERT: J 180 SER cc_start: 0.7956 (t) cc_final: 0.7584 (t) REVERT: J 248 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8201 (mt) REVERT: J 260 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7784 (mtt180) REVERT: J 281 MET cc_start: 0.8773 (mtp) cc_final: 0.8394 (mtm) REVERT: K 180 SER cc_start: 0.8238 (t) cc_final: 0.7953 (t) REVERT: K 217 ILE cc_start: 0.8352 (mt) cc_final: 0.8004 (mm) REVERT: K 261 ILE cc_start: 0.8382 (mt) cc_final: 0.8176 (mm) REVERT: K 288 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: K 294 MET cc_start: 0.8745 (pmm) cc_final: 0.8324 (pmm) REVERT: L 14 ASP cc_start: 0.8396 (t0) cc_final: 0.8001 (t70) REVERT: L 103 SER cc_start: 0.8538 (m) cc_final: 0.8067 (p) REVERT: L 248 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8177 (mt) REVERT: L 260 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7865 (mtm-85) REVERT: L 267 GLU cc_start: 0.7748 (tp30) cc_final: 0.7307 (tp30) REVERT: L 298 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8656 (mm-30) REVERT: L 314 SER cc_start: 0.7166 (OUTLIER) cc_final: 0.6955 (p) outliers start: 146 outliers final: 77 residues processed: 738 average time/residue: 0.6968 time to fit residues: 594.8365 Evaluate side-chains 703 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 611 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 192 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 339 optimal weight: 0.0570 chunk 44 optimal weight: 5.9990 chunk 311 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 97 GLN D 263 ASN E 130 HIS F 263 ASN G 263 ASN K 263 ASN L 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109855 restraints weight = 26438.064| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.69 r_work: 0.3002 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29076 Z= 0.115 Angle : 0.473 6.626 39396 Z= 0.254 Chirality : 0.046 0.170 4668 Planarity : 0.003 0.029 4992 Dihedral : 7.577 59.974 4290 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.29 % Allowed : 16.28 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.14), residues: 3660 helix: 2.29 (0.14), residues: 1404 sheet: -0.43 (0.17), residues: 996 loop : -0.18 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 22 TYR 0.012 0.001 TYR E 146 PHE 0.013 0.001 PHE C 35 TRP 0.007 0.001 TRP A 162 HIS 0.003 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00260 (29076) covalent geometry : angle 0.47350 (39396) hydrogen bonds : bond 0.03509 ( 1296) hydrogen bonds : angle 4.46437 ( 3600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 627 time to evaluate : 1.063 Fit side-chains REVERT: A 97 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: A 103 SER cc_start: 0.8249 (m) cc_final: 0.7809 (p) REVERT: A 132 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 180 SER cc_start: 0.7869 (t) cc_final: 0.7518 (t) REVERT: A 248 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8184 (mt) REVERT: A 260 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7755 (mtt180) REVERT: A 281 MET cc_start: 0.8826 (mtp) cc_final: 0.8444 (mtm) REVERT: A 288 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: B 14 ASP cc_start: 0.8190 (t0) cc_final: 0.7740 (t70) REVERT: B 52 ASP cc_start: 0.8746 (t0) cc_final: 0.8487 (t0) REVERT: B 79 ILE cc_start: 0.8932 (pt) cc_final: 0.8663 (mm) REVERT: B 191 LEU cc_start: 0.6761 (mp) cc_final: 0.6003 (tt) REVERT: C 115 MET cc_start: 0.9118 (mtp) cc_final: 0.8862 (mtp) REVERT: C 128 ASP cc_start: 0.8858 (m-30) cc_final: 0.8649 (m-30) REVERT: C 248 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8033 (mt) REVERT: C 260 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7495 (mtt90) REVERT: C 281 MET cc_start: 0.8636 (mtp) cc_final: 0.8166 (mtm) REVERT: C 294 MET cc_start: 0.8878 (pmm) cc_final: 0.8611 (pmm) REVERT: D 78 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: D 97 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: D 103 SER cc_start: 0.8361 (m) cc_final: 0.8063 (t) REVERT: D 245 TYR cc_start: 0.8572 (m-80) cc_final: 0.8209 (m-80) REVERT: D 261 ILE cc_start: 0.8361 (mt) cc_final: 0.8117 (mm) REVERT: D 267 GLU cc_start: 0.8238 (tp30) cc_final: 0.7821 (tp30) REVERT: D 292 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8531 (pp) REVERT: E 14 ASP cc_start: 0.8391 (t0) cc_final: 0.7986 (t70) REVERT: E 46 GLU cc_start: 0.8906 (pt0) cc_final: 0.8639 (pt0) REVERT: E 103 SER cc_start: 0.8569 (m) cc_final: 0.8086 (p) REVERT: E 180 SER cc_start: 0.7859 (t) cc_final: 0.7574 (t) REVERT: E 222 MET cc_start: 0.8574 (ptp) cc_final: 0.8158 (ptm) REVERT: E 248 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (mt) REVERT: E 260 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7723 (mtm-85) REVERT: E 267 GLU cc_start: 0.7738 (tp30) cc_final: 0.7263 (tp30) REVERT: F 180 SER cc_start: 0.8285 (t) cc_final: 0.8003 (t) REVERT: F 261 ILE cc_start: 0.8389 (mt) cc_final: 0.8175 (mm) REVERT: F 288 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: F 292 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8765 (pp) REVERT: F 294 MET cc_start: 0.8747 (pmm) cc_final: 0.8358 (pmm) REVERT: F 314 SER cc_start: 0.7132 (OUTLIER) cc_final: 0.6730 (p) REVERT: G 78 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8306 (ttmt) REVERT: G 97 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: G 245 TYR cc_start: 0.8498 (m-80) cc_final: 0.8160 (m-80) REVERT: G 292 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8528 (pp) REVERT: H 115 MET cc_start: 0.9134 (mtp) cc_final: 0.8878 (mtp) REVERT: H 248 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8026 (mt) REVERT: H 260 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7535 (mtm-85) REVERT: H 281 MET cc_start: 0.8670 (mtp) cc_final: 0.8208 (mtm) REVERT: H 294 MET cc_start: 0.8882 (pmm) cc_final: 0.8617 (pmm) REVERT: I 14 ASP cc_start: 0.8134 (t0) cc_final: 0.7874 (t70) REVERT: I 52 ASP cc_start: 0.8718 (t0) cc_final: 0.8463 (t0) REVERT: I 79 ILE cc_start: 0.8934 (pt) cc_final: 0.8661 (mm) REVERT: I 191 LEU cc_start: 0.6712 (mp) cc_final: 0.5967 (tt) REVERT: J 132 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8657 (t) REVERT: J 180 SER cc_start: 0.7918 (t) cc_final: 0.7561 (t) REVERT: J 248 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8286 (mt) REVERT: J 260 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7755 (mtt180) REVERT: J 281 MET cc_start: 0.8800 (mtp) cc_final: 0.8415 (mtm) REVERT: K 180 SER cc_start: 0.8197 (t) cc_final: 0.7926 (t) REVERT: K 217 ILE cc_start: 0.8327 (mt) cc_final: 0.7777 (mm) REVERT: K 261 ILE cc_start: 0.8383 (mt) cc_final: 0.8180 (mm) REVERT: K 288 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: K 292 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8758 (pp) REVERT: K 294 MET cc_start: 0.8730 (pmm) cc_final: 0.8274 (pmm) REVERT: K 314 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6725 (p) REVERT: L 14 ASP cc_start: 0.8436 (t0) cc_final: 0.8038 (t70) REVERT: L 103 SER cc_start: 0.8568 (m) cc_final: 0.8079 (p) REVERT: L 180 SER cc_start: 0.7850 (t) cc_final: 0.7558 (t) REVERT: L 222 MET cc_start: 0.8579 (ptp) cc_final: 0.8112 (ptm) REVERT: L 248 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8196 (mt) REVERT: L 260 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7747 (mtm-85) REVERT: L 267 GLU cc_start: 0.7738 (tp30) cc_final: 0.7270 (tp30) outliers start: 135 outliers final: 81 residues processed: 714 average time/residue: 0.6902 time to fit residues: 572.3959 Evaluate side-chains 708 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 605 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 320 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 12 HIS B 97 GLN B 135 GLN C 12 HIS C 97 GLN D 263 ASN E 12 HIS F 135 GLN F 263 ASN H 12 HIS H 97 GLN I 12 HIS I 135 GLN J 97 GLN J 288 GLN K 135 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104776 restraints weight = 26271.317| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.59 r_work: 0.2937 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 29076 Z= 0.260 Angle : 0.605 7.072 39396 Z= 0.324 Chirality : 0.051 0.186 4668 Planarity : 0.004 0.033 4992 Dihedral : 7.706 59.636 4290 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.38 % Allowed : 15.08 % Favored : 79.55 % 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: 0.79 (0.14), residues: 3660 helix: 2.11 (0.14), residues: 1404 sheet: -0.56 (0.17), residues: 996 loop : -0.24 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 22 TYR 0.019 0.003 TYR E 146 PHE 0.016 0.002 PHE G 138 TRP 0.008 0.002 TRP H 162 HIS 0.005 0.001 HIS G 123 Details of bonding type rmsd covalent geometry : bond 0.00610 (29076) covalent geometry : angle 0.60524 (39396) hydrogen bonds : bond 0.04689 ( 1296) hydrogen bonds : angle 4.57950 ( 3600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 605 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 103 SER cc_start: 0.8227 (m) cc_final: 0.7798 (p) REVERT: A 132 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8735 (t) REVERT: A 281 MET cc_start: 0.8767 (mtp) cc_final: 0.8330 (mtm) REVERT: A 288 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: B 14 ASP cc_start: 0.8251 (t0) cc_final: 0.7788 (t70) REVERT: B 52 ASP cc_start: 0.8722 (t0) cc_final: 0.8490 (t0) REVERT: B 191 LEU cc_start: 0.7260 (mp) cc_final: 0.6214 (tt) REVERT: B 288 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: B 314 SER cc_start: 0.7404 (OUTLIER) cc_final: 0.7103 (p) REVERT: C 115 MET cc_start: 0.9243 (mtp) cc_final: 0.8931 (mtp) REVERT: C 128 ASP cc_start: 0.8952 (m-30) cc_final: 0.8734 (m-30) REVERT: C 260 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7711 (mtt180) REVERT: C 294 MET cc_start: 0.8909 (pmm) cc_final: 0.8671 (pmm) REVERT: D 37 ASN cc_start: 0.8458 (p0) cc_final: 0.8228 (p0) REVERT: D 78 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8305 (ttmt) REVERT: D 97 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: D 103 SER cc_start: 0.8524 (m) cc_final: 0.8161 (t) REVERT: D 217 ILE cc_start: 0.8312 (mt) cc_final: 0.8008 (mm) REVERT: D 245 TYR cc_start: 0.8573 (m-80) cc_final: 0.8254 (m-80) REVERT: D 261 ILE cc_start: 0.8396 (mt) cc_final: 0.8144 (mm) REVERT: D 267 GLU cc_start: 0.8274 (tp30) cc_final: 0.7767 (tp30) REVERT: D 292 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8576 (pp) REVERT: E 13 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: E 14 ASP cc_start: 0.8414 (t0) cc_final: 0.7994 (t70) REVERT: E 46 GLU cc_start: 0.8933 (pt0) cc_final: 0.8644 (pt0) REVERT: E 103 SER cc_start: 0.8481 (m) cc_final: 0.8001 (p) REVERT: E 180 SER cc_start: 0.7812 (t) cc_final: 0.7517 (t) REVERT: E 267 GLU cc_start: 0.7728 (tp30) cc_final: 0.7234 (tp30) REVERT: E 278 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: F 39 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8254 (mt-10) REVERT: F 97 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: F 127 MET cc_start: 0.9183 (ttm) cc_final: 0.8825 (tpp) REVERT: F 180 SER cc_start: 0.8192 (t) cc_final: 0.7904 (t) REVERT: F 288 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: F 292 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8741 (pp) REVERT: F 314 SER cc_start: 0.7289 (OUTLIER) cc_final: 0.6854 (p) REVERT: G 14 ASP cc_start: 0.8171 (t70) cc_final: 0.7937 (t70) REVERT: G 78 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8304 (ttmt) REVERT: G 97 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: G 217 ILE cc_start: 0.8278 (mt) cc_final: 0.7994 (mm) REVERT: G 245 TYR cc_start: 0.8548 (m-80) cc_final: 0.8206 (m-80) REVERT: G 267 GLU cc_start: 0.8289 (tp30) cc_final: 0.7783 (tp30) REVERT: G 292 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8573 (pp) REVERT: H 39 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8176 (mt-10) REVERT: H 115 MET cc_start: 0.9259 (mtp) cc_final: 0.8952 (mtp) REVERT: H 260 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7705 (mtt180) REVERT: H 294 MET cc_start: 0.8913 (pmm) cc_final: 0.8674 (pmm) REVERT: I 14 ASP cc_start: 0.8243 (t0) cc_final: 0.8008 (t70) REVERT: I 52 ASP cc_start: 0.8696 (t0) cc_final: 0.8485 (t0) REVERT: I 97 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: I 314 SER cc_start: 0.7311 (OUTLIER) cc_final: 0.7000 (p) REVERT: J 13 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: J 132 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8705 (t) REVERT: J 180 SER cc_start: 0.7917 (t) cc_final: 0.7630 (t) REVERT: J 281 MET cc_start: 0.8750 (mtp) cc_final: 0.8328 (mtm) REVERT: J 286 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8232 (ptmt) REVERT: K 39 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8185 (mt-10) REVERT: K 97 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: K 217 ILE cc_start: 0.8447 (mt) cc_final: 0.7877 (mm) REVERT: K 288 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: K 292 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8741 (pp) REVERT: K 294 MET cc_start: 0.8671 (pmm) cc_final: 0.8336 (pmm) REVERT: K 314 SER cc_start: 0.7296 (OUTLIER) cc_final: 0.6866 (p) REVERT: L 13 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: L 14 ASP cc_start: 0.8451 (t0) cc_final: 0.8029 (t70) REVERT: L 103 SER cc_start: 0.8473 (m) cc_final: 0.7974 (p) REVERT: L 153 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7828 (tttm) REVERT: L 180 SER cc_start: 0.7791 (t) cc_final: 0.7496 (t) REVERT: L 267 GLU cc_start: 0.7721 (tp30) cc_final: 0.7235 (tp30) REVERT: L 278 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: L 288 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8326 (mp10) outliers start: 169 outliers final: 89 residues processed: 723 average time/residue: 0.7113 time to fit residues: 595.2043 Evaluate side-chains 712 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 594 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 91 optimal weight: 0.9980 chunk 295 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 349 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 97 GLN F 263 ASN H 97 GLN J 97 GLN J 288 GLN K 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107768 restraints weight = 26317.439| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.66 r_work: 0.2972 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29076 Z= 0.150 Angle : 0.507 6.549 39396 Z= 0.273 Chirality : 0.048 0.174 4668 Planarity : 0.003 0.032 4992 Dihedral : 7.185 59.579 4290 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.90 % Allowed : 15.33 % Favored : 79.77 % 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: 0.80 (0.14), residues: 3660 helix: 2.21 (0.14), residues: 1404 sheet: -0.61 (0.17), residues: 996 loop : -0.30 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 22 TYR 0.017 0.002 TYR L 146 PHE 0.013 0.002 PHE D 138 TRP 0.009 0.002 TRP L 162 HIS 0.004 0.001 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00343 (29076) covalent geometry : angle 0.50717 (39396) hydrogen bonds : bond 0.03797 ( 1296) hydrogen bonds : angle 4.46013 ( 3600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 613 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8306 (mm-40) REVERT: A 132 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8675 (t) REVERT: A 248 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 260 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7875 (mtt180) REVERT: A 281 MET cc_start: 0.8843 (mtp) cc_final: 0.8462 (mtm) REVERT: B 14 ASP cc_start: 0.8219 (t0) cc_final: 0.7760 (t70) REVERT: B 52 ASP cc_start: 0.8714 (t0) cc_final: 0.8450 (t0) REVERT: B 191 LEU cc_start: 0.6844 (mp) cc_final: 0.6088 (tt) REVERT: B 314 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 115 MET cc_start: 0.9206 (mtp) cc_final: 0.8905 (mtp) REVERT: C 128 ASP cc_start: 0.8891 (m-30) cc_final: 0.8648 (m-30) REVERT: C 248 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8086 (mt) REVERT: C 260 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7732 (mtt180) REVERT: C 294 MET cc_start: 0.8933 (pmm) cc_final: 0.8654 (pmm) REVERT: C 314 SER cc_start: 0.7398 (OUTLIER) cc_final: 0.6942 (p) REVERT: D 36 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7828 (t) REVERT: D 78 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8281 (ttmt) REVERT: D 96 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8470 (mtt180) REVERT: D 97 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: D 103 SER cc_start: 0.8388 (m) cc_final: 0.8043 (t) REVERT: D 245 TYR cc_start: 0.8491 (m-80) cc_final: 0.8199 (m-80) REVERT: D 261 ILE cc_start: 0.8389 (mt) cc_final: 0.8164 (mm) REVERT: D 267 GLU cc_start: 0.8247 (tp30) cc_final: 0.7756 (tp30) REVERT: D 292 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8536 (pp) REVERT: E 13 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: E 14 ASP cc_start: 0.8397 (t0) cc_final: 0.7988 (t70) REVERT: E 46 GLU cc_start: 0.8905 (pt0) cc_final: 0.8597 (pt0) REVERT: E 103 SER cc_start: 0.8535 (m) cc_final: 0.8002 (p) REVERT: E 180 SER cc_start: 0.7816 (t) cc_final: 0.7548 (t) REVERT: E 222 MET cc_start: 0.8616 (ptp) cc_final: 0.8312 (ptp) REVERT: E 248 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8187 (mt) REVERT: E 267 GLU cc_start: 0.7665 (tp30) cc_final: 0.7201 (tp30) REVERT: E 278 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: E 314 SER cc_start: 0.7102 (OUTLIER) cc_final: 0.6863 (p) REVERT: F 97 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: F 180 SER cc_start: 0.8182 (t) cc_final: 0.7930 (t) REVERT: F 224 ASP cc_start: 0.8707 (t0) cc_final: 0.8430 (t0) REVERT: F 288 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: F 292 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8771 (pp) REVERT: F 314 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6745 (p) REVERT: G 78 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8293 (ttmt) REVERT: G 97 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: G 245 TYR cc_start: 0.8502 (m-80) cc_final: 0.8210 (m-80) REVERT: G 267 GLU cc_start: 0.8270 (tp30) cc_final: 0.7770 (tp30) REVERT: G 292 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8533 (pp) REVERT: H 115 MET cc_start: 0.9226 (mtp) cc_final: 0.8927 (mtp) REVERT: H 222 MET cc_start: 0.8592 (ptp) cc_final: 0.8315 (ptm) REVERT: H 248 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8086 (mt) REVERT: H 260 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7614 (mtt90) REVERT: H 294 MET cc_start: 0.8930 (pmm) cc_final: 0.8652 (pmm) REVERT: I 14 ASP cc_start: 0.8197 (t0) cc_final: 0.7920 (t70) REVERT: I 52 ASP cc_start: 0.8687 (t0) cc_final: 0.8416 (t0) REVERT: I 267 GLU cc_start: 0.8221 (tp30) cc_final: 0.7992 (tp30) REVERT: I 314 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6921 (p) REVERT: J 13 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: J 132 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8649 (t) REVERT: J 180 SER cc_start: 0.7904 (t) cc_final: 0.7623 (t) REVERT: J 248 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8133 (mt) REVERT: J 260 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7898 (mtt180) REVERT: J 281 MET cc_start: 0.8811 (mtp) cc_final: 0.8409 (mtm) REVERT: K 97 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: K 180 SER cc_start: 0.8124 (t) cc_final: 0.7869 (t) REVERT: K 217 ILE cc_start: 0.8385 (mt) cc_final: 0.7801 (mm) REVERT: K 288 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: K 292 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8730 (pp) REVERT: K 294 MET cc_start: 0.8731 (pmm) cc_final: 0.8395 (pmm) REVERT: K 314 SER cc_start: 0.7187 (OUTLIER) cc_final: 0.6771 (p) REVERT: L 13 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: L 14 ASP cc_start: 0.8439 (t0) cc_final: 0.8016 (t70) REVERT: L 22 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8717 (mtt-85) REVERT: L 103 SER cc_start: 0.8491 (m) cc_final: 0.8006 (p) REVERT: L 153 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7772 (tttm) REVERT: L 180 SER cc_start: 0.7802 (t) cc_final: 0.7513 (t) REVERT: L 248 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8191 (mt) REVERT: L 267 GLU cc_start: 0.7666 (tp30) cc_final: 0.7210 (tp30) REVERT: L 278 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: L 288 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8354 (mp10) outliers start: 154 outliers final: 90 residues processed: 720 average time/residue: 0.6680 time to fit residues: 559.4293 Evaluate side-chains 717 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 593 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 284 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 130 HIS F 263 ASN J 97 GLN J 288 GLN K 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.157133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107856 restraints weight = 26279.560| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.61 r_work: 0.2969 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29076 Z= 0.136 Angle : 0.496 6.820 39396 Z= 0.266 Chirality : 0.047 0.170 4668 Planarity : 0.003 0.031 4992 Dihedral : 6.996 59.038 4290 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.77 % Allowed : 15.78 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3660 helix: 2.29 (0.14), residues: 1404 sheet: -0.64 (0.17), residues: 996 loop : -0.34 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 22 TYR 0.016 0.002 TYR L 146 PHE 0.012 0.001 PHE G 138 TRP 0.009 0.002 TRP E 162 HIS 0.003 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00311 (29076) covalent geometry : angle 0.49641 (39396) hydrogen bonds : bond 0.03669 ( 1296) hydrogen bonds : angle 4.42074 ( 3600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 600 time to evaluate : 1.164 Fit side-chains REVERT: A 13 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: A 51 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8509 (mm-30) REVERT: A 97 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8284 (mm-40) REVERT: A 132 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8679 (t) REVERT: A 260 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7882 (mtt180) REVERT: A 281 MET cc_start: 0.8827 (mtp) cc_final: 0.8448 (mtm) REVERT: B 14 ASP cc_start: 0.8222 (t0) cc_final: 0.7784 (t70) REVERT: B 52 ASP cc_start: 0.8683 (t0) cc_final: 0.8408 (t0) REVERT: B 288 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: B 314 SER cc_start: 0.7232 (OUTLIER) cc_final: 0.6961 (p) REVERT: C 51 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8613 (mm-30) REVERT: C 115 MET cc_start: 0.9227 (mtp) cc_final: 0.8905 (mtp) REVERT: C 128 ASP cc_start: 0.8879 (m-30) cc_final: 0.8591 (m-30) REVERT: C 248 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8124 (mt) REVERT: C 260 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7727 (mtt180) REVERT: C 294 MET cc_start: 0.8913 (pmm) cc_final: 0.8569 (pmm) REVERT: C 314 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.6957 (p) REVERT: D 78 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8287 (ttmt) REVERT: D 96 ARG cc_start: 0.8727 (mtm180) cc_final: 0.8443 (mtt180) REVERT: D 97 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: D 103 SER cc_start: 0.8418 (m) cc_final: 0.8074 (t) REVERT: D 217 ILE cc_start: 0.8277 (mt) cc_final: 0.7936 (mm) REVERT: D 245 TYR cc_start: 0.8504 (m-80) cc_final: 0.8234 (m-80) REVERT: D 261 ILE cc_start: 0.8402 (mt) cc_final: 0.8170 (mm) REVERT: D 267 GLU cc_start: 0.8244 (tp30) cc_final: 0.7756 (tp30) REVERT: D 277 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8490 (mm110) REVERT: D 288 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: D 292 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8534 (pp) REVERT: E 13 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: E 14 ASP cc_start: 0.8390 (t0) cc_final: 0.7989 (t70) REVERT: E 46 GLU cc_start: 0.8927 (pt0) cc_final: 0.8639 (pt0) REVERT: E 103 SER cc_start: 0.8447 (m) cc_final: 0.7934 (p) REVERT: E 180 SER cc_start: 0.7840 (t) cc_final: 0.7587 (t) REVERT: E 222 MET cc_start: 0.8626 (ptp) cc_final: 0.8375 (ptp) REVERT: E 267 GLU cc_start: 0.7690 (tp30) cc_final: 0.7226 (tp30) REVERT: E 278 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: F 97 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: F 127 MET cc_start: 0.9168 (ttm) cc_final: 0.8836 (tpp) REVERT: F 180 SER cc_start: 0.8216 (t) cc_final: 0.7952 (t) REVERT: F 224 ASP cc_start: 0.8713 (t0) cc_final: 0.8413 (t0) REVERT: F 278 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: F 288 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: F 292 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8755 (pp) REVERT: F 314 SER cc_start: 0.7150 (OUTLIER) cc_final: 0.6739 (p) REVERT: G 78 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8293 (ttmt) REVERT: G 97 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: G 224 ASP cc_start: 0.8591 (t0) cc_final: 0.8337 (t0) REVERT: G 245 TYR cc_start: 0.8497 (m-80) cc_final: 0.8230 (m-80) REVERT: G 267 GLU cc_start: 0.8280 (tp30) cc_final: 0.7789 (tp30) REVERT: G 292 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8531 (pp) REVERT: H 115 MET cc_start: 0.9238 (mtp) cc_final: 0.8919 (mtp) REVERT: H 222 MET cc_start: 0.8581 (ptp) cc_final: 0.8359 (ptm) REVERT: H 248 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8048 (mt) REVERT: H 260 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7611 (mtt90) REVERT: H 294 MET cc_start: 0.8912 (pmm) cc_final: 0.8566 (pmm) REVERT: I 14 ASP cc_start: 0.8169 (t0) cc_final: 0.7908 (t70) REVERT: I 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8396 (t0) REVERT: I 97 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: I 314 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6884 (p) REVERT: J 13 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: J 132 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8659 (t) REVERT: J 248 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8115 (mt) REVERT: J 260 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7898 (mtt180) REVERT: J 281 MET cc_start: 0.8805 (mtp) cc_final: 0.8435 (mtm) REVERT: K 97 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: K 180 SER cc_start: 0.8166 (t) cc_final: 0.7903 (t) REVERT: K 288 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: K 294 MET cc_start: 0.8736 (pmm) cc_final: 0.8388 (pmm) REVERT: K 314 SER cc_start: 0.7186 (OUTLIER) cc_final: 0.6771 (p) REVERT: L 13 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: L 14 ASP cc_start: 0.8426 (t0) cc_final: 0.8007 (t70) REVERT: L 22 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8687 (mtt-85) REVERT: L 103 SER cc_start: 0.8515 (m) cc_final: 0.7980 (p) REVERT: L 153 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7765 (tttm) REVERT: L 180 SER cc_start: 0.7818 (t) cc_final: 0.7562 (t) REVERT: L 260 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7867 (mtm180) REVERT: L 267 GLU cc_start: 0.7674 (tp30) cc_final: 0.7226 (tp30) REVERT: L 278 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: L 288 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8347 (mp10) outliers start: 150 outliers final: 90 residues processed: 709 average time/residue: 0.6617 time to fit residues: 543.8921 Evaluate side-chains 715 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 592 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 318 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 12 HIS B 97 GLN C 12 HIS E 12 HIS F 263 ASN H 12 HIS I 12 HIS J 97 GLN J 288 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104801 restraints weight = 26411.676| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.56 r_work: 0.2924 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29076 Z= 0.259 Angle : 0.607 7.328 39396 Z= 0.324 Chirality : 0.051 0.181 4668 Planarity : 0.004 0.048 4992 Dihedral : 7.285 58.312 4287 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.77 % Allowed : 15.87 % Favored : 79.36 % 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: 0.64 (0.14), residues: 3660 helix: 2.09 (0.14), residues: 1404 sheet: -0.76 (0.16), residues: 996 loop : -0.36 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 22 TYR 0.022 0.003 TYR L 146 PHE 0.021 0.002 PHE H 35 TRP 0.008 0.002 TRP L 162 HIS 0.004 0.001 HIS G 123 Details of bonding type rmsd covalent geometry : bond 0.00609 (29076) covalent geometry : angle 0.60687 (39396) hydrogen bonds : bond 0.04630 ( 1296) hydrogen bonds : angle 4.54985 ( 3600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 603 time to evaluate : 1.064 Fit side-chains REVERT: A 13 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 132 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8702 (t) REVERT: A 260 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7780 (mtt180) REVERT: A 281 MET cc_start: 0.8730 (mtp) cc_final: 0.8286 (mtm) REVERT: B 14 ASP cc_start: 0.8257 (t0) cc_final: 0.7783 (t70) REVERT: B 52 ASP cc_start: 0.8713 (t0) cc_final: 0.8447 (t0) REVERT: B 97 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8393 (mt0) REVERT: B 282 LYS cc_start: 0.7826 (mttp) cc_final: 0.7394 (mtpm) REVERT: B 288 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: B 314 SER cc_start: 0.7352 (OUTLIER) cc_final: 0.7074 (p) REVERT: C 115 MET cc_start: 0.9284 (mtp) cc_final: 0.8898 (mtp) REVERT: C 128 ASP cc_start: 0.8961 (m-30) cc_final: 0.8746 (m-30) REVERT: C 260 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7633 (mtt90) REVERT: C 294 MET cc_start: 0.8895 (pmm) cc_final: 0.8648 (pmm) REVERT: C 314 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.7104 (p) REVERT: D 37 ASN cc_start: 0.8554 (p0) cc_final: 0.8313 (p0) REVERT: D 78 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8307 (ttmt) REVERT: D 97 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: D 103 SER cc_start: 0.8543 (m) cc_final: 0.8162 (t) REVERT: D 217 ILE cc_start: 0.8303 (mt) cc_final: 0.7986 (mm) REVERT: D 245 TYR cc_start: 0.8574 (m-80) cc_final: 0.8277 (m-80) REVERT: D 261 ILE cc_start: 0.8425 (mt) cc_final: 0.8148 (mm) REVERT: D 267 GLU cc_start: 0.8229 (tp30) cc_final: 0.7710 (tp30) REVERT: D 288 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: D 292 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8531 (pp) REVERT: E 13 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: E 14 ASP cc_start: 0.8415 (t0) cc_final: 0.7980 (t70) REVERT: E 46 GLU cc_start: 0.8886 (pt0) cc_final: 0.8602 (pt0) REVERT: E 180 SER cc_start: 0.7786 (t) cc_final: 0.7516 (t) REVERT: E 267 GLU cc_start: 0.7712 (tp30) cc_final: 0.7303 (tp30) REVERT: E 278 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: F 68 MET cc_start: 0.8901 (mmm) cc_final: 0.8678 (tpp) REVERT: F 97 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: F 127 MET cc_start: 0.9177 (ttm) cc_final: 0.8799 (tpp) REVERT: F 217 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8148 (mm) REVERT: F 288 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: F 292 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8796 (pp) REVERT: F 314 SER cc_start: 0.7227 (OUTLIER) cc_final: 0.6743 (p) REVERT: G 78 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: G 97 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: G 217 ILE cc_start: 0.8300 (mt) cc_final: 0.7988 (mm) REVERT: G 245 TYR cc_start: 0.8569 (m-80) cc_final: 0.8272 (m-80) REVERT: G 267 GLU cc_start: 0.8303 (tp30) cc_final: 0.7775 (tp30) REVERT: G 292 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8539 (pp) REVERT: H 97 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8567 (mm-40) REVERT: H 115 MET cc_start: 0.9296 (mtp) cc_final: 0.8915 (mtp) REVERT: H 260 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7554 (mtt90) REVERT: H 294 MET cc_start: 0.8907 (pmm) cc_final: 0.8646 (pmm) REVERT: I 14 ASP cc_start: 0.8229 (t0) cc_final: 0.7983 (t70) REVERT: I 52 ASP cc_start: 0.8669 (t0) cc_final: 0.8422 (t0) REVERT: I 97 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: I 314 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.6953 (p) REVERT: J 13 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: J 132 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8666 (t) REVERT: J 260 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7773 (mtt180) REVERT: J 281 MET cc_start: 0.8741 (mtp) cc_final: 0.8301 (mtm) REVERT: K 39 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8415 (mt-10) REVERT: K 97 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: K 217 ILE cc_start: 0.8326 (mt) cc_final: 0.8081 (mm) REVERT: K 288 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: K 292 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8741 (pp) REVERT: K 294 MET cc_start: 0.8673 (pmm) cc_final: 0.8327 (pmm) REVERT: K 314 SER cc_start: 0.7228 (OUTLIER) cc_final: 0.6752 (p) REVERT: L 13 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: L 14 ASP cc_start: 0.8450 (t0) cc_final: 0.8023 (t70) REVERT: L 180 SER cc_start: 0.7768 (t) cc_final: 0.7482 (t) REVERT: L 278 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: L 288 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8301 (mp10) outliers start: 150 outliers final: 89 residues processed: 706 average time/residue: 0.6927 time to fit residues: 567.7267 Evaluate side-chains 719 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 598 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 283 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 286 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 97 GLN F 263 ASN J 97 GLN J 288 GLN K 263 ASN K 305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107779 restraints weight = 26471.960| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.56 r_work: 0.2969 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29076 Z= 0.139 Angle : 0.503 6.417 39396 Z= 0.270 Chirality : 0.047 0.171 4668 Planarity : 0.003 0.041 4992 Dihedral : 6.750 55.490 4284 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.26 % Allowed : 16.60 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3660 helix: 2.22 (0.14), residues: 1404 sheet: -0.80 (0.16), residues: 996 loop : -0.36 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 22 TYR 0.019 0.002 TYR L 146 PHE 0.018 0.001 PHE H 35 TRP 0.010 0.002 TRP L 162 HIS 0.003 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00318 (29076) covalent geometry : angle 0.50264 (39396) hydrogen bonds : bond 0.03674 ( 1296) hydrogen bonds : angle 4.42872 ( 3600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 601 time to evaluate : 1.080 Fit side-chains REVERT: A 13 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: A 132 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8643 (t) REVERT: A 260 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7825 (mtt180) REVERT: A 281 MET cc_start: 0.8809 (mtp) cc_final: 0.8420 (mtm) REVERT: B 14 ASP cc_start: 0.8246 (t0) cc_final: 0.7776 (t70) REVERT: B 52 ASP cc_start: 0.8685 (t0) cc_final: 0.8411 (t0) REVERT: B 282 LYS cc_start: 0.7859 (mttp) cc_final: 0.7415 (mtpm) REVERT: B 288 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: B 314 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 115 MET cc_start: 0.9221 (mtp) cc_final: 0.8887 (mtp) REVERT: C 128 ASP cc_start: 0.8900 (m-30) cc_final: 0.8638 (m-30) REVERT: C 248 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8117 (mt) REVERT: C 260 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7737 (mtt180) REVERT: C 294 MET cc_start: 0.8891 (pmm) cc_final: 0.8549 (pmm) REVERT: D 78 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8299 (ttmt) REVERT: D 97 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: D 103 SER cc_start: 0.8423 (m) cc_final: 0.8065 (t) REVERT: D 217 ILE cc_start: 0.8269 (mt) cc_final: 0.7899 (mm) REVERT: D 245 TYR cc_start: 0.8520 (m-80) cc_final: 0.8240 (m-80) REVERT: D 261 ILE cc_start: 0.8390 (mt) cc_final: 0.8176 (mm) REVERT: D 267 GLU cc_start: 0.8208 (tp30) cc_final: 0.7705 (tp30) REVERT: D 277 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8461 (mm110) REVERT: D 292 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8520 (pp) REVERT: E 13 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: E 14 ASP cc_start: 0.8390 (t0) cc_final: 0.7976 (t70) REVERT: E 46 GLU cc_start: 0.8874 (pt0) cc_final: 0.8598 (pt0) REVERT: E 180 SER cc_start: 0.7810 (t) cc_final: 0.7551 (t) REVERT: E 222 MET cc_start: 0.8624 (ptp) cc_final: 0.8304 (ptp) REVERT: E 248 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (mt) REVERT: E 267 GLU cc_start: 0.7693 (tp30) cc_final: 0.7253 (tp30) REVERT: E 278 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: F 97 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: F 102 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8676 (mttp) REVERT: F 127 MET cc_start: 0.9140 (ttm) cc_final: 0.8798 (tpp) REVERT: F 224 ASP cc_start: 0.8678 (t0) cc_final: 0.8456 (t0) REVERT: F 278 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: F 288 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: F 292 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8770 (pp) REVERT: F 314 SER cc_start: 0.7131 (OUTLIER) cc_final: 0.6723 (p) REVERT: G 78 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8298 (ttmt) REVERT: G 97 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: G 245 TYR cc_start: 0.8507 (m-80) cc_final: 0.8233 (m-80) REVERT: G 267 GLU cc_start: 0.8255 (tp30) cc_final: 0.7744 (tp30) REVERT: G 292 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8528 (pp) REVERT: H 115 MET cc_start: 0.9234 (mtp) cc_final: 0.8905 (mtp) REVERT: H 222 MET cc_start: 0.8637 (ptp) cc_final: 0.8393 (ptm) REVERT: H 260 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7581 (mtt90) REVERT: H 294 MET cc_start: 0.8899 (pmm) cc_final: 0.8635 (pmm) REVERT: H 314 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.6915 (p) REVERT: I 14 ASP cc_start: 0.8180 (t0) cc_final: 0.7908 (t70) REVERT: I 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8378 (t0) REVERT: I 97 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: I 314 SER cc_start: 0.7100 (OUTLIER) cc_final: 0.6819 (p) REVERT: J 13 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: J 132 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8607 (t) REVERT: J 248 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8080 (mt) REVERT: J 260 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7827 (mtt180) REVERT: J 281 MET cc_start: 0.8779 (mtp) cc_final: 0.8390 (mtm) REVERT: K 97 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: K 217 ILE cc_start: 0.8276 (mt) cc_final: 0.8033 (mm) REVERT: K 288 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: K 292 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8752 (pp) REVERT: K 294 MET cc_start: 0.8717 (pmm) cc_final: 0.8383 (pmm) REVERT: K 314 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6736 (p) REVERT: L 13 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: L 14 ASP cc_start: 0.8424 (t0) cc_final: 0.8015 (t70) REVERT: L 127 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8907 (ttp) REVERT: L 180 SER cc_start: 0.7783 (t) cc_final: 0.7526 (t) REVERT: L 248 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8206 (mt) REVERT: L 278 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: L 288 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8294 (mp10) outliers start: 134 outliers final: 85 residues processed: 698 average time/residue: 0.7138 time to fit residues: 577.2599 Evaluate side-chains 712 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 592 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 299 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 135 optimal weight: 7.9990 chunk 286 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 357 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN F 263 ASN H 130 HIS J 97 GLN J 288 GLN K 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110053 restraints weight = 26487.511| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.53 r_work: 0.2997 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29076 Z= 0.105 Angle : 0.474 7.789 39396 Z= 0.252 Chirality : 0.046 0.168 4668 Planarity : 0.003 0.033 4992 Dihedral : 6.477 54.503 4284 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.82 % Allowed : 17.24 % Favored : 78.94 % 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: 0.81 (0.14), residues: 3660 helix: 2.37 (0.14), residues: 1404 sheet: -0.76 (0.17), residues: 996 loop : -0.35 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 22 TYR 0.015 0.001 TYR L 146 PHE 0.016 0.001 PHE H 35 TRP 0.011 0.002 TRP E 162 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00235 (29076) covalent geometry : angle 0.47364 (39396) hydrogen bonds : bond 0.03268 ( 1296) hydrogen bonds : angle 4.32462 ( 3600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 631 time to evaluate : 1.090 Fit side-chains REVERT: A 21 ASP cc_start: 0.8388 (m-30) cc_final: 0.8114 (m-30) REVERT: A 96 ARG cc_start: 0.8723 (mtm180) cc_final: 0.8497 (mtm180) REVERT: A 103 SER cc_start: 0.8241 (m) cc_final: 0.7774 (p) REVERT: A 132 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8638 (t) REVERT: A 260 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7892 (mtt180) REVERT: A 281 MET cc_start: 0.8811 (mtp) cc_final: 0.8443 (mtm) REVERT: B 14 ASP cc_start: 0.8173 (t0) cc_final: 0.7715 (t70) REVERT: B 38 GLN cc_start: 0.8330 (mm110) cc_final: 0.8049 (mm110) REVERT: B 52 ASP cc_start: 0.8699 (t0) cc_final: 0.8460 (t0) REVERT: B 79 ILE cc_start: 0.8981 (pt) cc_final: 0.8713 (mm) REVERT: B 282 LYS cc_start: 0.7888 (mttp) cc_final: 0.7427 (mtpm) REVERT: B 288 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: B 314 SER cc_start: 0.7089 (OUTLIER) cc_final: 0.6838 (p) REVERT: C 115 MET cc_start: 0.9177 (mtp) cc_final: 0.8806 (mtp) REVERT: C 128 ASP cc_start: 0.8856 (m-30) cc_final: 0.8609 (m-30) REVERT: C 222 MET cc_start: 0.8605 (ptp) cc_final: 0.8313 (ptm) REVERT: C 248 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8091 (mt) REVERT: C 260 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7651 (mtt180) REVERT: C 294 MET cc_start: 0.8898 (pmm) cc_final: 0.8585 (pmm) REVERT: D 68 MET cc_start: 0.8622 (tpp) cc_final: 0.8375 (tpt) REVERT: D 78 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8320 (ttmt) REVERT: D 96 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8357 (mtt180) REVERT: D 97 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: D 103 SER cc_start: 0.8401 (m) cc_final: 0.8060 (t) REVERT: D 217 ILE cc_start: 0.8255 (mt) cc_final: 0.7907 (mm) REVERT: D 261 ILE cc_start: 0.8375 (mt) cc_final: 0.8170 (mm) REVERT: D 267 GLU cc_start: 0.8181 (tp30) cc_final: 0.7701 (tp30) REVERT: D 277 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8401 (mm110) REVERT: D 288 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: D 292 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8552 (pp) REVERT: E 13 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: E 14 ASP cc_start: 0.8357 (t0) cc_final: 0.7939 (t70) REVERT: E 46 GLU cc_start: 0.8876 (pt0) cc_final: 0.8607 (pt0) REVERT: E 180 SER cc_start: 0.7766 (t) cc_final: 0.7523 (t) REVERT: E 222 MET cc_start: 0.8601 (ptp) cc_final: 0.8304 (ptp) REVERT: E 248 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8196 (mt) REVERT: E 260 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7647 (mtm-85) REVERT: E 267 GLU cc_start: 0.7692 (tp30) cc_final: 0.7212 (tp30) REVERT: E 278 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: F 102 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8572 (mttp) REVERT: F 127 MET cc_start: 0.9132 (ttm) cc_final: 0.8790 (tpp) REVERT: F 180 SER cc_start: 0.8302 (t) cc_final: 0.8013 (t) REVERT: F 191 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6007 (tm) REVERT: F 278 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: F 288 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: F 292 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8749 (pp) REVERT: F 314 SER cc_start: 0.7034 (OUTLIER) cc_final: 0.6614 (p) REVERT: G 68 MET cc_start: 0.8622 (tpp) cc_final: 0.8379 (tpt) REVERT: G 78 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8296 (ttmt) REVERT: G 103 SER cc_start: 0.8399 (m) cc_final: 0.8047 (t) REVERT: G 267 GLU cc_start: 0.8241 (tp30) cc_final: 0.7752 (tp30) REVERT: G 292 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8553 (pp) REVERT: H 115 MET cc_start: 0.9191 (mtp) cc_final: 0.8825 (mtp) REVERT: H 260 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7516 (mtt90) REVERT: H 294 MET cc_start: 0.8885 (pmm) cc_final: 0.8582 (pmm) REVERT: H 314 SER cc_start: 0.7327 (OUTLIER) cc_final: 0.6860 (p) REVERT: I 14 ASP cc_start: 0.8122 (t0) cc_final: 0.7875 (t70) REVERT: I 52 ASP cc_start: 0.8678 (t0) cc_final: 0.8424 (t0) REVERT: I 79 ILE cc_start: 0.8931 (pt) cc_final: 0.8703 (mm) REVERT: I 282 LYS cc_start: 0.7902 (mttp) cc_final: 0.7460 (mtpm) REVERT: I 314 SER cc_start: 0.7005 (OUTLIER) cc_final: 0.6730 (p) REVERT: J 132 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8606 (t) REVERT: J 260 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7885 (mtt180) REVERT: J 281 MET cc_start: 0.8789 (mtp) cc_final: 0.8395 (mtm) REVERT: K 97 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: K 180 SER cc_start: 0.8261 (t) cc_final: 0.7980 (t) REVERT: K 217 ILE cc_start: 0.8235 (mt) cc_final: 0.7969 (mm) REVERT: K 282 LYS cc_start: 0.7829 (tttt) cc_final: 0.7221 (ttpp) REVERT: K 288 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: K 292 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8770 (pp) REVERT: K 294 MET cc_start: 0.8742 (pmm) cc_final: 0.8309 (pmm) REVERT: K 314 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6629 (p) REVERT: L 14 ASP cc_start: 0.8394 (t0) cc_final: 0.7990 (t70) REVERT: L 180 SER cc_start: 0.7727 (t) cc_final: 0.7486 (t) REVERT: L 248 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8198 (mt) REVERT: L 260 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7681 (mtm-85) REVERT: L 267 GLU cc_start: 0.7690 (tp30) cc_final: 0.7233 (tp30) REVERT: L 278 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: L 288 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8306 (mp10) outliers start: 120 outliers final: 77 residues processed: 718 average time/residue: 0.7190 time to fit residues: 597.9974 Evaluate side-chains 716 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 610 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 102 LYS Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 88 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 288 GLN B 97 GLN F 263 ASN G 277 GLN I 17 GLN J 97 GLN J 288 GLN K 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108309 restraints weight = 26547.037| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.55 r_work: 0.2976 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29076 Z= 0.135 Angle : 0.506 8.100 39396 Z= 0.268 Chirality : 0.047 0.170 4668 Planarity : 0.003 0.040 4992 Dihedral : 6.486 57.045 4284 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.75 % Allowed : 17.53 % Favored : 78.72 % 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: 0.81 (0.14), residues: 3660 helix: 2.37 (0.14), residues: 1404 sheet: -0.79 (0.17), residues: 996 loop : -0.34 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 22 TYR 0.016 0.002 TYR L 146 PHE 0.017 0.001 PHE C 35 TRP 0.010 0.002 TRP E 162 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00311 (29076) covalent geometry : angle 0.50563 (39396) hydrogen bonds : bond 0.03607 ( 1296) hydrogen bonds : angle 4.33598 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15529.46 seconds wall clock time: 263 minutes 45.80 seconds (15825.80 seconds total)