Starting phenix.real_space_refine on Mon May 26 14:57:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbm_27290/05_2025/8dbm_27290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbm_27290/05_2025/8dbm_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_27290/05_2025/8dbm_27290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbm_27290/05_2025/8dbm_27290.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbm_27290/05_2025/8dbm_27290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbm_27290/05_2025/8dbm_27290.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.10, per 1000 atoms: 0.56 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: 7.74 Conformation dependent library (CDL) restraints added in 3.9 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: 4.28 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: 10.35 Time building geometry restraints manager: 8.97 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: 0.27 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 0.990 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: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 64.160 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.003 TRP E 162 HIS 0.003 0.001 HIS D 193 PHE 0.017 0.002 PHE K 138 TYR 0.027 0.004 TYR C 245 ARG 0.004 0.001 ARG I 177 Details of bonding type rmsd hydrogen bonds : bond 0.15501 ( 1296) hydrogen bonds : angle 5.67951 ( 3600) covalent geometry : bond 0.01102 (29076) covalent geometry : angle 0.82343 (39396) *********************** 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 : 2.963 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: 0.8352 (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: 0.8351 (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: 0.8229 (mtt180) cc_final: 0.7880 (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: 0.8150 (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: 1.3651 time to fit residues: 1423.4958 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 : 3.046 ------------------------------------------------------------------------------- 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 303 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 0.8980 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 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 = 0.171990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125517 restraints weight = 26197.913| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.61 r_work: 0.3200 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 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 = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29076 Z= 0.142 Angle : 0.509 5.679 39396 Z= 0.277 Chirality : 0.048 0.173 4668 Planarity : 0.003 0.022 4992 Dihedral : 8.798 68.032 4318 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.25 % Allowed : 13.90 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3660 helix: 1.97 (0.14), residues: 1404 sheet: -0.47 (0.17), residues: 996 loop : -0.01 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 162 HIS 0.004 0.001 HIS F 123 PHE 0.012 0.001 PHE H 35 TYR 0.013 0.002 TYR A 311 ARG 0.003 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1296) hydrogen bonds : angle 4.79646 ( 3600) covalent geometry : bond 0.00314 (29076) covalent geometry : angle 0.50915 (39396) *********************** 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 824 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 659 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8759 (mmmt) REVERT: A 13 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: A 103 SER cc_start: 0.8328 (m) cc_final: 0.7867 (p) REVERT: A 128 ASP cc_start: 0.8896 (m-30) cc_final: 0.8673 (m-30) REVERT: A 180 SER cc_start: 0.7851 (t) cc_final: 0.7458 (t) REVERT: A 248 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 260 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7826 (mtt180) REVERT: A 281 MET cc_start: 0.8778 (mtp) cc_final: 0.8408 (mtm) REVERT: B 14 ASP cc_start: 0.8272 (t0) cc_final: 0.7846 (t70) REVERT: B 52 ASP cc_start: 0.8829 (t0) cc_final: 0.8589 (t0) REVERT: B 191 LEU cc_start: 0.6930 (mp) cc_final: 0.5903 (tt) REVERT: B 288 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: C 5 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8701 (mmmt) REVERT: C 13 GLN cc_start: 0.8488 (tp40) cc_final: 0.8267 (mm-40) REVERT: C 128 ASP cc_start: 0.8948 (m-30) cc_final: 0.8716 (m-30) REVERT: C 176 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6684 (ttmt) REVERT: C 248 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8068 (mt) REVERT: C 260 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7741 (mtm-85) REVERT: C 281 MET cc_start: 0.8680 (mtp) cc_final: 0.8110 (mtm) REVERT: C 288 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: C 294 MET cc_start: 0.8922 (pmm) cc_final: 0.8640 (pmm) REVERT: D 78 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8328 (ttmt) REVERT: D 97 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: D 158 ASN cc_start: 0.8078 (m-40) cc_final: 0.7573 (m110) REVERT: D 261 ILE cc_start: 0.8396 (mt) cc_final: 0.8112 (mm) REVERT: E 14 ASP cc_start: 0.8429 (t0) cc_final: 0.8029 (t70) REVERT: E 46 GLU cc_start: 0.8973 (pt0) cc_final: 0.8727 (pt0) REVERT: E 103 SER cc_start: 0.8493 (m) cc_final: 0.8045 (p) REVERT: E 180 SER cc_start: 0.7831 (t) cc_final: 0.7502 (t) REVERT: E 260 ARG cc_start: 0.8282 (mtt180) cc_final: 0.8044 (mtt180) REVERT: E 267 GLU cc_start: 0.7791 (tp30) cc_final: 0.7369 (tp30) REVERT: E 282 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8262 (mmtp) REVERT: F 97 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: F 180 SER cc_start: 0.8298 (t) cc_final: 0.8069 (t) REVERT: F 259 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8091 (p) REVERT: F 261 ILE cc_start: 0.8529 (mt) cc_final: 0.8274 (mm) REVERT: F 294 MET cc_start: 0.8811 (pmm) cc_final: 0.8435 (pmm) REVERT: G 78 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8350 (ttmt) REVERT: G 96 ARG cc_start: 0.8705 (mtm180) cc_final: 0.8492 (mtm180) REVERT: G 97 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: G 158 ASN cc_start: 0.8147 (m-40) cc_final: 0.7626 (m110) REVERT: G 261 ILE cc_start: 0.8370 (mt) cc_final: 0.8114 (mm) REVERT: H 5 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8676 (mmtp) REVERT: H 13 GLN cc_start: 0.8540 (tp40) cc_final: 0.8294 (mm-40) REVERT: H 128 ASP cc_start: 0.8957 (m-30) cc_final: 0.8636 (m-30) REVERT: H 176 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6666 (ttmt) REVERT: H 248 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8091 (mt) REVERT: H 260 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7737 (mtm-85) REVERT: H 281 MET cc_start: 0.8685 (mtp) cc_final: 0.8107 (mtm) REVERT: H 288 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: H 294 MET cc_start: 0.8928 (pmm) cc_final: 0.8646 (pmm) REVERT: I 14 ASP cc_start: 0.8238 (t0) cc_final: 0.8012 (t70) REVERT: I 97 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: I 191 LEU cc_start: 0.6920 (mp) cc_final: 0.5916 (tt) REVERT: I 288 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: J 5 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8759 (mmmt) REVERT: J 103 SER cc_start: 0.8303 (m) cc_final: 0.7852 (p) REVERT: J 128 ASP cc_start: 0.8893 (m-30) cc_final: 0.8670 (m-30) REVERT: J 180 SER cc_start: 0.7917 (t) cc_final: 0.7523 (t) REVERT: J 248 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8286 (mt) REVERT: J 260 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7853 (mtt180) REVERT: J 281 MET cc_start: 0.8760 (mtp) cc_final: 0.8389 (mtm) REVERT: K 97 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: K 180 SER cc_start: 0.8265 (t) cc_final: 0.8044 (t) REVERT: K 217 ILE cc_start: 0.8228 (mt) cc_final: 0.7992 (mm) REVERT: K 259 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8088 (p) REVERT: K 261 ILE cc_start: 0.8492 (mt) cc_final: 0.8260 (mm) REVERT: K 294 MET cc_start: 0.8785 (pmm) cc_final: 0.8403 (pmm) REVERT: L 14 ASP cc_start: 0.8453 (t0) cc_final: 0.8056 (t70) REVERT: L 35 PHE cc_start: 0.8543 (m-80) cc_final: 0.8304 (m-80) REVERT: L 103 SER cc_start: 0.8505 (m) cc_final: 0.8058 (p) REVERT: L 180 SER cc_start: 0.7830 (t) cc_final: 0.7494 (t) REVERT: L 260 ARG cc_start: 0.8298 (mtt180) cc_final: 0.8067 (mtt180) REVERT: L 267 GLU cc_start: 0.7794 (tp30) cc_final: 0.7393 (tp30) outliers start: 165 outliers final: 90 residues processed: 768 average time/residue: 1.3941 time to fit residues: 1246.6298 Evaluate side-chains 736 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 621 time to evaluate : 2.984 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 285 SER 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 78 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 290 optimal weight: 0.5980 chunk 338 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 B 17 GLN B 135 GLN 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 I 135 GLN J 97 GLN K 130 HIS K 263 ASN L 130 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108679 restraints weight = 26130.709| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.57 r_work: 0.2985 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29076 Z= 0.164 Angle : 0.523 5.996 39396 Z= 0.282 Chirality : 0.048 0.175 4668 Planarity : 0.003 0.026 4992 Dihedral : 8.174 58.102 4310 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.06 % Allowed : 14.57 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3660 helix: 2.12 (0.14), residues: 1404 sheet: -0.44 (0.17), residues: 996 loop : -0.12 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.004 0.001 HIS F 12 PHE 0.013 0.002 PHE D 138 TYR 0.016 0.002 TYR L 146 ARG 0.006 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1296) hydrogen bonds : angle 4.59321 ( 3600) covalent geometry : bond 0.00376 (29076) covalent geometry : angle 0.52314 (39396) *********************** 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 789 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 630 time to evaluate : 3.002 Fit side-chains REVERT: A 13 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: A 97 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8245 (mm-40) REVERT: A 103 SER cc_start: 0.8281 (m) cc_final: 0.7861 (p) REVERT: A 132 SER cc_start: 0.8924 (p) cc_final: 0.8679 (t) REVERT: A 180 SER cc_start: 0.7832 (t) cc_final: 0.7421 (t) REVERT: A 248 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 260 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7724 (mtt180) REVERT: A 281 MET cc_start: 0.8861 (mtp) cc_final: 0.8471 (mtm) REVERT: B 14 ASP cc_start: 0.8237 (t0) cc_final: 0.7772 (t70) REVERT: B 52 ASP cc_start: 0.8766 (t0) cc_final: 0.8528 (t0) REVERT: B 62 GLU cc_start: 0.8096 (tp30) cc_final: 0.7854 (tp30) REVERT: B 191 LEU cc_start: 0.6894 (mp) cc_final: 0.6078 (tt) REVERT: B 288 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: C 5 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8657 (mmmt) REVERT: C 35 PHE cc_start: 0.8424 (m-80) cc_final: 0.8173 (m-80) REVERT: C 115 MET cc_start: 0.9091 (mtp) cc_final: 0.8814 (mtp) REVERT: C 128 ASP cc_start: 0.8912 (m-30) cc_final: 0.8666 (m-30) REVERT: C 259 SER cc_start: 0.8327 (m) cc_final: 0.8117 (m) REVERT: C 260 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7653 (mtt180) REVERT: C 288 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: C 294 MET cc_start: 0.8903 (pmm) cc_final: 0.8546 (pmm) REVERT: D 78 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8291 (ttmt) REVERT: D 97 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: D 103 SER cc_start: 0.8347 (m) cc_final: 0.8023 (t) REVERT: D 245 TYR cc_start: 0.8574 (m-80) cc_final: 0.8252 (m-80) REVERT: D 261 ILE cc_start: 0.8382 (mt) cc_final: 0.8122 (mm) REVERT: E 13 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: E 14 ASP cc_start: 0.8400 (t0) cc_final: 0.8002 (t70) REVERT: E 46 GLU cc_start: 0.8880 (pt0) cc_final: 0.8563 (pt0) REVERT: E 103 SER cc_start: 0.8583 (m) cc_final: 0.8129 (p) REVERT: E 180 SER cc_start: 0.7887 (t) cc_final: 0.7583 (t) REVERT: E 222 MET cc_start: 0.8500 (ptp) cc_final: 0.8141 (ptm) REVERT: E 267 GLU cc_start: 0.7750 (tp30) cc_final: 0.7281 (tp30) REVERT: F 97 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: F 180 SER cc_start: 0.8252 (t) cc_final: 0.7955 (t) REVERT: F 288 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: F 314 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.6829 (p) REVERT: G 78 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8279 (ttmt) REVERT: G 97 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: G 103 SER cc_start: 0.8348 (m) cc_final: 0.8019 (t) REVERT: G 245 TYR cc_start: 0.8554 (m-80) cc_final: 0.8225 (m-80) REVERT: G 261 ILE cc_start: 0.8365 (mt) cc_final: 0.8129 (mm) REVERT: H 5 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8704 (mmmt) REVERT: H 13 GLN cc_start: 0.8505 (tp40) cc_final: 0.8239 (mm-40) REVERT: H 35 PHE cc_start: 0.8437 (m-80) cc_final: 0.8211 (m-80) REVERT: H 115 MET cc_start: 0.9101 (mtp) cc_final: 0.8824 (mtp) REVERT: H 128 ASP cc_start: 0.8909 (m-30) cc_final: 0.8665 (m-30) REVERT: H 260 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7626 (mtt180) REVERT: H 288 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: H 294 MET cc_start: 0.8908 (pmm) cc_final: 0.8551 (pmm) REVERT: I 14 ASP cc_start: 0.8202 (t0) cc_final: 0.7934 (t70) REVERT: I 52 ASP cc_start: 0.8747 (t0) cc_final: 0.8509 (t0) REVERT: I 97 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: I 191 LEU cc_start: 0.7024 (mp) cc_final: 0.6010 (tt) REVERT: J 13 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: J 97 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8246 (mm-40) REVERT: J 103 SER cc_start: 0.8245 (m) cc_final: 0.7824 (p) REVERT: J 132 SER cc_start: 0.8928 (p) cc_final: 0.8666 (t) REVERT: J 180 SER cc_start: 0.7946 (t) cc_final: 0.7579 (t) REVERT: J 260 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7740 (mtt180) REVERT: J 281 MET cc_start: 0.8843 (mtp) cc_final: 0.8453 (mtm) REVERT: K 97 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: K 180 SER cc_start: 0.8206 (t) cc_final: 0.7908 (t) REVERT: K 217 ILE cc_start: 0.8407 (mt) cc_final: 0.8106 (mm) REVERT: K 288 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: K 314 SER cc_start: 0.7246 (OUTLIER) cc_final: 0.6847 (p) REVERT: L 13 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: L 14 ASP cc_start: 0.8430 (t0) cc_final: 0.8036 (t70) REVERT: L 35 PHE cc_start: 0.8536 (m-80) cc_final: 0.8272 (m-80) REVERT: L 103 SER cc_start: 0.8581 (m) cc_final: 0.8125 (p) REVERT: L 180 SER cc_start: 0.7886 (t) cc_final: 0.7576 (t) REVERT: L 267 GLU cc_start: 0.7752 (tp30) cc_final: 0.7287 (tp30) REVERT: L 314 SER cc_start: 0.7270 (OUTLIER) cc_final: 0.7037 (p) outliers start: 159 outliers final: 87 residues processed: 733 average time/residue: 1.4080 time to fit residues: 1201.2489 Evaluate side-chains 716 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 605 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 288 GLN Chi-restraints excluded: chain B residue 307 GLU 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 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 288 GLN Chi-restraints excluded: chain C residue 314 SER 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 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 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 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 12 HIS 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 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 314 SER Chi-restraints excluded: chain G residue 12 HIS 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 G residue 314 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 97 GLN 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 H residue 314 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 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 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 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 314 SER 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 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 118 VAL Chi-restraints excluded: chain L residue 132 SER 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 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 280 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 341 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 12 HIS D 263 ASN E 12 HIS F 263 ASN H 12 HIS H 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107452 restraints weight = 26352.458| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.64 r_work: 0.2966 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29076 Z= 0.163 Angle : 0.516 5.472 39396 Z= 0.279 Chirality : 0.048 0.175 4668 Planarity : 0.003 0.029 4992 Dihedral : 7.617 58.688 4298 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.03 % Allowed : 14.73 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3660 helix: 2.16 (0.14), residues: 1404 sheet: -0.51 (0.17), residues: 996 loop : -0.20 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 162 HIS 0.003 0.001 HIS F 12 PHE 0.013 0.002 PHE G 138 TYR 0.017 0.002 TYR L 146 ARG 0.006 0.000 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1296) hydrogen bonds : angle 4.53113 ( 3600) covalent geometry : bond 0.00376 (29076) covalent geometry : angle 0.51586 (39396) *********************** 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 775 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 617 time to evaluate : 3.249 Fit side-chains REVERT: A 13 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: A 97 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: A 132 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8717 (t) REVERT: A 180 SER cc_start: 0.7835 (t) cc_final: 0.7489 (t) REVERT: A 248 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 260 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7694 (mtt180) REVERT: A 281 MET cc_start: 0.8817 (mtp) cc_final: 0.8405 (mtm) REVERT: A 288 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: B 14 ASP cc_start: 0.8265 (t0) cc_final: 0.7783 (t70) REVERT: B 52 ASP cc_start: 0.8745 (t0) cc_final: 0.8513 (t0) REVERT: B 62 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: B 191 LEU cc_start: 0.6873 (mp) cc_final: 0.6053 (tt) REVERT: B 267 GLU cc_start: 0.8179 (tp30) cc_final: 0.7949 (tp30) REVERT: B 314 SER cc_start: 0.7384 (OUTLIER) cc_final: 0.7068 (p) REVERT: C 5 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8611 (mmmt) REVERT: C 115 MET cc_start: 0.9168 (mtp) cc_final: 0.8860 (mtp) REVERT: C 128 ASP cc_start: 0.8896 (m-30) cc_final: 0.8666 (m-30) REVERT: C 248 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8051 (mt) REVERT: C 260 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7677 (mtt180) REVERT: C 288 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: C 294 MET cc_start: 0.8924 (pmm) cc_final: 0.8571 (pmm) REVERT: D 78 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8282 (ttmt) REVERT: D 97 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: D 103 SER cc_start: 0.8382 (m) cc_final: 0.8044 (t) REVERT: D 245 TYR cc_start: 0.8536 (m-80) cc_final: 0.8217 (m-80) REVERT: D 261 ILE cc_start: 0.8388 (mt) cc_final: 0.8161 (mm) REVERT: D 267 GLU cc_start: 0.8250 (tp30) cc_final: 0.7816 (tp30) REVERT: D 292 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8562 (pp) REVERT: E 14 ASP cc_start: 0.8422 (t0) cc_final: 0.8020 (t70) REVERT: E 46 GLU cc_start: 0.8875 (pt0) cc_final: 0.8576 (pt0) REVERT: E 103 SER cc_start: 0.8533 (m) cc_final: 0.8073 (p) REVERT: E 153 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7794 (tttm) REVERT: E 180 SER cc_start: 0.7866 (t) cc_final: 0.7577 (t) REVERT: E 222 MET cc_start: 0.8562 (ptp) cc_final: 0.8104 (ptm) REVERT: E 248 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8200 (mt) REVERT: E 267 GLU cc_start: 0.7739 (tp30) cc_final: 0.7252 (tp30) REVERT: F 39 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8273 (mt-10) REVERT: F 97 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: F 127 MET cc_start: 0.9177 (ttm) cc_final: 0.8838 (tpp) REVERT: F 180 SER cc_start: 0.8206 (t) cc_final: 0.7941 (t) REVERT: F 288 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: F 292 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8712 (pp) REVERT: F 314 SER cc_start: 0.7162 (OUTLIER) cc_final: 0.6780 (p) REVERT: G 78 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8286 (ttmt) REVERT: G 97 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: G 103 SER cc_start: 0.8374 (m) cc_final: 0.8023 (t) REVERT: G 245 TYR cc_start: 0.8524 (m-80) cc_final: 0.8253 (m-80) REVERT: G 261 ILE cc_start: 0.8351 (mt) cc_final: 0.8123 (mm) REVERT: G 292 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8558 (pp) REVERT: H 5 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8636 (mmmt) REVERT: H 13 GLN cc_start: 0.8479 (tp40) cc_final: 0.8204 (mm-40) REVERT: H 115 MET cc_start: 0.9172 (mtp) cc_final: 0.8871 (mtp) REVERT: H 128 ASP cc_start: 0.8870 (m-30) cc_final: 0.8637 (m-30) REVERT: H 248 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8050 (mt) REVERT: H 260 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7663 (mtt180) REVERT: H 288 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: H 294 MET cc_start: 0.8919 (pmm) cc_final: 0.8571 (pmm) REVERT: I 14 ASP cc_start: 0.8230 (t0) cc_final: 0.7950 (t70) REVERT: I 52 ASP cc_start: 0.8723 (t0) cc_final: 0.8482 (t0) REVERT: I 97 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: I 267 GLU cc_start: 0.8220 (tp30) cc_final: 0.7975 (tp30) REVERT: I 314 SER cc_start: 0.7285 (OUTLIER) cc_final: 0.6964 (p) REVERT: J 13 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: J 97 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8134 (mm-40) REVERT: J 132 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8693 (t) REVERT: J 180 SER cc_start: 0.7917 (t) cc_final: 0.7548 (t) REVERT: J 248 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8235 (mt) REVERT: J 260 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7719 (mtt180) REVERT: J 281 MET cc_start: 0.8829 (mtp) cc_final: 0.8433 (mtm) REVERT: J 288 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: K 97 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: K 180 SER cc_start: 0.8155 (t) cc_final: 0.7885 (t) REVERT: K 217 ILE cc_start: 0.8382 (mt) cc_final: 0.7805 (mm) REVERT: K 288 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: K 292 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8734 (pp) REVERT: K 314 SER cc_start: 0.7167 (OUTLIER) cc_final: 0.6766 (p) REVERT: L 14 ASP cc_start: 0.8450 (t0) cc_final: 0.8052 (t70) REVERT: L 103 SER cc_start: 0.8551 (m) cc_final: 0.8082 (p) REVERT: L 153 LYS cc_start: 0.8041 (ttpp) cc_final: 0.7802 (tttm) REVERT: L 180 SER cc_start: 0.7876 (t) cc_final: 0.7585 (t) REVERT: L 222 MET cc_start: 0.8605 (ptp) cc_final: 0.8132 (ptm) REVERT: L 248 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8198 (mt) REVERT: L 267 GLU cc_start: 0.7724 (tp30) cc_final: 0.7253 (tp30) REVERT: L 314 SER cc_start: 0.7133 (OUTLIER) cc_final: 0.6889 (p) outliers start: 158 outliers final: 93 residues processed: 725 average time/residue: 1.4148 time to fit residues: 1204.7168 Evaluate side-chains 733 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 603 time to evaluate : 2.970 ------------------------------------------------------------------------------- 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 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 62 GLU Chi-restraints excluded: chain B residue 97 GLN 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 314 SER Chi-restraints excluded: chain C residue 5 LYS 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 258 ILE 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 C residue 292 ILE Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 12 HIS 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 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 132 SER 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 314 SER 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 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 12 HIS 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 5 LYS 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 258 ILE 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 H residue 292 ILE Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 62 GLU 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 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 288 GLN Chi-restraints excluded: chain J residue 314 SER 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 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 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 Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 229 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 296 optimal weight: 0.4980 chunk 283 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 331 optimal weight: 4.9990 chunk 136 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN D 263 ASN F 263 ASN J 97 GLN K 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109997 restraints weight = 26447.598| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.67 r_work: 0.2994 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29076 Z= 0.110 Angle : 0.469 5.921 39396 Z= 0.253 Chirality : 0.046 0.168 4668 Planarity : 0.003 0.029 4992 Dihedral : 7.188 59.933 4298 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.45 % Allowed : 15.81 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3660 helix: 2.27 (0.14), residues: 1404 sheet: -0.54 (0.17), residues: 996 loop : -0.28 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 162 HIS 0.003 0.001 HIS G 12 PHE 0.012 0.001 PHE L 35 TYR 0.013 0.001 TYR L 146 ARG 0.007 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 1296) hydrogen bonds : angle 4.43226 ( 3600) covalent geometry : bond 0.00245 (29076) covalent geometry : angle 0.46942 (39396) *********************** 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 752 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 612 time to evaluate : 3.166 Fit side-chains REVERT: A 51 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 132 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8683 (t) REVERT: A 248 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 281 MET cc_start: 0.8819 (mtp) cc_final: 0.8449 (mtm) REVERT: B 14 ASP cc_start: 0.8205 (t0) cc_final: 0.7753 (t70) REVERT: B 52 ASP cc_start: 0.8730 (t0) cc_final: 0.8492 (t0) REVERT: B 62 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: B 79 ILE cc_start: 0.8939 (pt) cc_final: 0.8662 (mm) REVERT: B 191 LEU cc_start: 0.6711 (mp) cc_final: 0.5924 (tt) REVERT: B 267 GLU cc_start: 0.8065 (tp30) cc_final: 0.7846 (tp30) REVERT: B 314 SER cc_start: 0.7224 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 115 MET cc_start: 0.9149 (mtp) cc_final: 0.8922 (mtp) REVERT: C 128 ASP cc_start: 0.8866 (m-30) cc_final: 0.8644 (m-30) REVERT: C 222 MET cc_start: 0.8560 (ptp) cc_final: 0.8274 (ptm) REVERT: C 248 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8052 (mt) REVERT: C 260 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7551 (mtt90) REVERT: C 294 MET cc_start: 0.8900 (pmm) cc_final: 0.8567 (pmm) REVERT: D 78 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8286 (ttmt) REVERT: D 97 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: D 103 SER cc_start: 0.8385 (m) cc_final: 0.8057 (t) REVERT: D 245 TYR cc_start: 0.8501 (m-80) cc_final: 0.8200 (m-80) REVERT: D 261 ILE cc_start: 0.8341 (mt) cc_final: 0.8130 (mm) REVERT: D 267 GLU cc_start: 0.8223 (tp30) cc_final: 0.7738 (tp30) REVERT: D 292 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8554 (pp) REVERT: E 13 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: E 14 ASP cc_start: 0.8391 (t0) cc_final: 0.7987 (t70) REVERT: E 46 GLU cc_start: 0.8895 (pt0) cc_final: 0.8594 (pt0) REVERT: E 103 SER cc_start: 0.8478 (m) cc_final: 0.8010 (p) REVERT: E 153 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7795 (tttm) REVERT: E 180 SER cc_start: 0.7867 (t) cc_final: 0.7609 (t) REVERT: E 222 MET cc_start: 0.8568 (ptp) cc_final: 0.8288 (ptp) REVERT: E 248 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8150 (mt) REVERT: E 260 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7765 (mtm-85) REVERT: E 267 GLU cc_start: 0.7737 (tp30) cc_final: 0.7236 (tp30) REVERT: F 180 SER cc_start: 0.8218 (t) cc_final: 0.7970 (t) REVERT: F 288 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: F 292 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8775 (pp) REVERT: G 78 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: G 97 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: G 245 TYR cc_start: 0.8488 (m-80) cc_final: 0.8211 (m-80) REVERT: G 261 ILE cc_start: 0.8351 (mt) cc_final: 0.8134 (mm) REVERT: G 267 GLU cc_start: 0.8254 (tp30) cc_final: 0.7827 (tp30) REVERT: G 292 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8519 (pp) REVERT: H 115 MET cc_start: 0.9156 (mtp) cc_final: 0.8934 (mtp) REVERT: H 128 ASP cc_start: 0.8873 (m-30) cc_final: 0.8639 (m-30) REVERT: H 248 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8039 (mt) REVERT: H 260 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7522 (mtt90) REVERT: H 294 MET cc_start: 0.8913 (pmm) cc_final: 0.8580 (pmm) REVERT: I 14 ASP cc_start: 0.8157 (t0) cc_final: 0.7882 (t70) REVERT: I 52 ASP cc_start: 0.8708 (t0) cc_final: 0.8446 (t0) REVERT: I 79 ILE cc_start: 0.8928 (pt) cc_final: 0.8651 (mm) REVERT: I 267 GLU cc_start: 0.8173 (tp30) cc_final: 0.7935 (tp30) REVERT: I 314 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6874 (p) REVERT: J 97 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8055 (mm-40) REVERT: J 132 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8655 (t) REVERT: J 180 SER cc_start: 0.7889 (t) cc_final: 0.7613 (t) REVERT: J 248 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8086 (mt) REVERT: J 281 MET cc_start: 0.8820 (mtp) cc_final: 0.8453 (mtm) REVERT: J 288 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: K 180 SER cc_start: 0.8174 (t) cc_final: 0.7929 (t) REVERT: K 288 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: K 292 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8777 (pp) REVERT: K 294 MET cc_start: 0.8670 (pmm) cc_final: 0.8428 (pmm) REVERT: L 14 ASP cc_start: 0.8397 (t0) cc_final: 0.7981 (t70) REVERT: L 103 SER cc_start: 0.8522 (m) cc_final: 0.8046 (p) REVERT: L 180 SER cc_start: 0.7856 (t) cc_final: 0.7608 (t) REVERT: L 222 MET cc_start: 0.8603 (ptp) cc_final: 0.8323 (ptp) REVERT: L 248 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8152 (mt) REVERT: L 260 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7790 (mtm-85) REVERT: L 267 GLU cc_start: 0.7701 (tp30) cc_final: 0.7221 (tp30) REVERT: L 288 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8370 (mp10) outliers start: 140 outliers final: 75 residues processed: 709 average time/residue: 1.3892 time to fit residues: 1149.9095 Evaluate side-chains 696 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 596 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 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 62 GLU 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 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 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 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 E residue 13 GLN 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 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 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 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 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 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 288 GLN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 77 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 332 optimal weight: 0.0170 chunk 205 optimal weight: 0.7980 chunk 342 optimal weight: 4.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- 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 D 277 GLN F 263 ASN J 97 GLN K 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108874 restraints weight = 26423.917| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.67 r_work: 0.2981 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- 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 = 0.54 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 = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29076 Z= 0.128 Angle : 0.488 6.571 39396 Z= 0.261 Chirality : 0.047 0.170 4668 Planarity : 0.003 0.029 4992 Dihedral : 6.962 59.372 4290 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.71 % Allowed : 16.32 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3660 helix: 2.34 (0.14), residues: 1404 sheet: -0.58 (0.17), residues: 996 loop : -0.33 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS E 304 PHE 0.012 0.001 PHE D 138 TYR 0.014 0.002 TYR L 146 ARG 0.007 0.000 ARG I 184 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1296) hydrogen bonds : angle 4.40727 ( 3600) covalent geometry : bond 0.00292 (29076) covalent geometry : angle 0.48754 (39396) *********************** 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 746 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 598 time to evaluate : 3.489 Fit side-chains REVERT: A 51 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8503 (mm-30) REVERT: A 132 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8691 (t) REVERT: A 248 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8125 (mt) REVERT: A 260 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7804 (mtt180) REVERT: A 281 MET cc_start: 0.8830 (mtp) cc_final: 0.8443 (mtm) REVERT: B 14 ASP cc_start: 0.8204 (t0) cc_final: 0.7744 (t70) REVERT: B 52 ASP cc_start: 0.8720 (t0) cc_final: 0.8478 (t0) REVERT: B 62 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: B 314 SER cc_start: 0.7203 (OUTLIER) cc_final: 0.6914 (p) REVERT: C 115 MET cc_start: 0.9198 (mtp) cc_final: 0.8944 (mtp) REVERT: C 128 ASP cc_start: 0.8886 (m-30) cc_final: 0.8645 (m-30) REVERT: C 222 MET cc_start: 0.8560 (ptp) cc_final: 0.8277 (ptm) REVERT: C 248 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8119 (mt) REVERT: C 260 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7702 (mtt180) REVERT: C 294 MET cc_start: 0.8896 (pmm) cc_final: 0.8553 (pmm) REVERT: C 314 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.6915 (p) REVERT: D 78 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8294 (ttmt) REVERT: D 97 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: D 103 SER cc_start: 0.8397 (m) cc_final: 0.8070 (t) REVERT: D 217 ILE cc_start: 0.8262 (mt) cc_final: 0.7932 (mm) REVERT: D 245 TYR cc_start: 0.8500 (m-80) cc_final: 0.8212 (m-80) REVERT: D 261 ILE cc_start: 0.8358 (mt) cc_final: 0.8132 (mm) REVERT: D 267 GLU cc_start: 0.8244 (tp30) cc_final: 0.7822 (tp30) REVERT: D 292 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8554 (pp) REVERT: E 13 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: E 14 ASP cc_start: 0.8401 (t0) cc_final: 0.8000 (t70) REVERT: E 46 GLU cc_start: 0.8941 (pt0) cc_final: 0.8653 (pt0) REVERT: E 97 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: E 103 SER cc_start: 0.8437 (m) cc_final: 0.7907 (p) REVERT: E 153 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7810 (tttm) REVERT: E 180 SER cc_start: 0.7881 (t) cc_final: 0.7628 (t) REVERT: E 222 MET cc_start: 0.8585 (ptp) cc_final: 0.8330 (ptp) REVERT: E 260 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7728 (mtm-85) REVERT: E 267 GLU cc_start: 0.7705 (tp30) cc_final: 0.7228 (tp30) REVERT: E 278 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: F 127 MET cc_start: 0.9169 (ttm) cc_final: 0.8845 (tpp) REVERT: F 180 SER cc_start: 0.8242 (t) cc_final: 0.7989 (t) REVERT: F 288 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: F 292 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8774 (pp) REVERT: G 78 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8281 (ttmt) REVERT: G 97 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: G 245 TYR cc_start: 0.8510 (m-80) cc_final: 0.8217 (m-80) REVERT: G 261 ILE cc_start: 0.8369 (mt) cc_final: 0.8155 (mm) REVERT: G 267 GLU cc_start: 0.8268 (tp30) cc_final: 0.7790 (tp30) REVERT: G 292 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8593 (pp) REVERT: H 39 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8199 (mt-10) REVERT: H 97 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8460 (mm-40) REVERT: H 115 MET cc_start: 0.9208 (mtp) cc_final: 0.8925 (mtp) REVERT: H 128 ASP cc_start: 0.8881 (m-30) cc_final: 0.8641 (m-30) REVERT: H 248 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8040 (mt) REVERT: H 260 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7666 (mtt180) REVERT: H 294 MET cc_start: 0.8908 (pmm) cc_final: 0.8634 (pmm) REVERT: I 14 ASP cc_start: 0.8163 (t0) cc_final: 0.7899 (t70) REVERT: I 52 ASP cc_start: 0.8704 (t0) cc_final: 0.8441 (t0) REVERT: I 62 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: I 267 GLU cc_start: 0.8086 (tp30) cc_final: 0.7869 (tp30) REVERT: I 288 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: I 314 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6878 (p) REVERT: J 13 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: J 97 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8219 (mm-40) REVERT: J 132 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8672 (t) REVERT: J 180 SER cc_start: 0.7839 (t) cc_final: 0.7571 (t) REVERT: J 248 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8091 (mt) REVERT: J 260 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7805 (mtt180) REVERT: J 281 MET cc_start: 0.8827 (mtp) cc_final: 0.8453 (mtm) REVERT: K 180 SER cc_start: 0.8133 (t) cc_final: 0.7879 (t) REVERT: K 217 ILE cc_start: 0.8221 (mt) cc_final: 0.8019 (mm) REVERT: K 288 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: K 292 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8774 (pp) REVERT: K 294 MET cc_start: 0.8669 (pmm) cc_final: 0.8396 (pmm) REVERT: L 13 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: L 14 ASP cc_start: 0.8421 (t0) cc_final: 0.8027 (t70) REVERT: L 103 SER cc_start: 0.8470 (m) cc_final: 0.7939 (p) REVERT: L 153 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7801 (tttm) REVERT: L 180 SER cc_start: 0.7876 (t) cc_final: 0.7625 (t) REVERT: L 222 MET cc_start: 0.8635 (ptp) cc_final: 0.8393 (ptp) REVERT: L 260 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7754 (mtm-85) REVERT: L 267 GLU cc_start: 0.7680 (tp30) cc_final: 0.7222 (tp30) REVERT: L 278 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: L 288 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8394 (mp10) outliers start: 148 outliers final: 84 residues processed: 698 average time/residue: 1.3793 time to fit residues: 1130.4923 Evaluate side-chains 703 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 588 time to evaluate : 3.101 ------------------------------------------------------------------------------- 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 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 62 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 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 258 ILE 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 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 97 GLN 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 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 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 97 GLN 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 258 ILE 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 62 GLU 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 288 GLN 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 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 L residue 13 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 339 optimal weight: 0.0670 chunk 167 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 332 optimal weight: 0.3980 chunk 304 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.8924 ------------------------------------------------------------------------------- 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 J 97 GLN K 135 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 = 0.3757 r_free = 0.3757 target = 0.156227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107812 restraints weight = 26266.442| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.65 r_work: 0.2955 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29076 Z= 0.172 Angle : 0.527 6.898 39396 Z= 0.281 Chirality : 0.048 0.175 4668 Planarity : 0.003 0.031 4992 Dihedral : 7.086 58.963 4290 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.74 % Allowed : 16.19 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3660 helix: 2.31 (0.14), residues: 1404 sheet: -0.62 (0.17), residues: 996 loop : -0.33 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 162 HIS 0.003 0.001 HIS H 123 PHE 0.013 0.002 PHE E 35 TYR 0.017 0.002 TYR L 146 ARG 0.006 0.001 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1296) hydrogen bonds : angle 4.43232 ( 3600) covalent geometry : bond 0.00397 (29076) covalent geometry : angle 0.52739 (39396) *********************** 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 744 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 595 time to evaluate : 3.007 Fit side-chains REVERT: A 13 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 132 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8693 (t) REVERT: A 281 MET cc_start: 0.8820 (mtp) cc_final: 0.8451 (mtm) REVERT: B 14 ASP cc_start: 0.8231 (t0) cc_final: 0.7769 (t70) REVERT: B 52 ASP cc_start: 0.8710 (t0) cc_final: 0.8443 (t0) REVERT: B 62 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: B 97 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: B 314 SER cc_start: 0.7257 (OUTLIER) cc_final: 0.6974 (p) REVERT: C 115 MET cc_start: 0.9257 (mtp) cc_final: 0.8860 (mtp) REVERT: C 128 ASP cc_start: 0.8896 (m-30) cc_final: 0.8643 (m-30) REVERT: C 248 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8145 (mt) REVERT: C 260 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7728 (mtt180) REVERT: C 294 MET cc_start: 0.8925 (pmm) cc_final: 0.8684 (pmm) REVERT: C 314 SER cc_start: 0.7447 (OUTLIER) cc_final: 0.7008 (p) REVERT: D 78 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8279 (ttmt) REVERT: D 97 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: D 103 SER cc_start: 0.8506 (m) cc_final: 0.8128 (t) REVERT: D 217 ILE cc_start: 0.8267 (mt) cc_final: 0.7937 (mm) REVERT: D 245 TYR cc_start: 0.8520 (m-80) cc_final: 0.8242 (m-80) REVERT: D 261 ILE cc_start: 0.8377 (mt) cc_final: 0.8157 (mm) REVERT: D 267 GLU cc_start: 0.8261 (tp30) cc_final: 0.7768 (tp30) REVERT: D 292 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8537 (pp) REVERT: E 13 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: E 14 ASP cc_start: 0.8393 (t0) cc_final: 0.7976 (t70) REVERT: E 46 GLU cc_start: 0.8897 (pt0) cc_final: 0.8621 (pt0) REVERT: E 97 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: E 103 SER cc_start: 0.8394 (m) cc_final: 0.7897 (p) REVERT: E 153 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7815 (tttm) REVERT: E 180 SER cc_start: 0.7828 (t) cc_final: 0.7575 (t) REVERT: E 222 MET cc_start: 0.8590 (ptp) cc_final: 0.8165 (ptm) REVERT: E 267 GLU cc_start: 0.7701 (tp30) cc_final: 0.7236 (tp30) REVERT: E 278 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: E 314 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6936 (p) REVERT: F 127 MET cc_start: 0.9172 (ttm) cc_final: 0.8828 (tpp) REVERT: F 180 SER cc_start: 0.8196 (t) cc_final: 0.7928 (t) REVERT: F 278 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: F 292 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8786 (pp) REVERT: F 314 SER cc_start: 0.7207 (OUTLIER) cc_final: 0.6765 (p) REVERT: G 78 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8278 (ttmt) REVERT: G 97 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: G 217 ILE cc_start: 0.8267 (mt) cc_final: 0.7937 (mm) REVERT: G 245 TYR cc_start: 0.8537 (m-80) cc_final: 0.8247 (m-80) REVERT: G 261 ILE cc_start: 0.8395 (mt) cc_final: 0.8158 (mm) REVERT: G 267 GLU cc_start: 0.8280 (tp30) cc_final: 0.7782 (tp30) REVERT: G 292 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8529 (pp) REVERT: H 115 MET cc_start: 0.9266 (mtp) cc_final: 0.8882 (mtp) REVERT: H 128 ASP cc_start: 0.8893 (m-30) cc_final: 0.8644 (m-30) REVERT: H 222 MET cc_start: 0.8542 (ptp) cc_final: 0.8283 (ptm) REVERT: H 248 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8063 (mt) REVERT: H 260 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7625 (mtm-85) REVERT: H 294 MET cc_start: 0.8931 (pmm) cc_final: 0.8670 (pmm) REVERT: I 14 ASP cc_start: 0.8179 (t0) cc_final: 0.7892 (t70) REVERT: I 52 ASP cc_start: 0.8681 (t0) cc_final: 0.8418 (t0) REVERT: I 62 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: I 97 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: I 267 GLU cc_start: 0.8124 (tp30) cc_final: 0.7900 (tp30) REVERT: I 288 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: I 314 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6876 (p) REVERT: J 13 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: J 97 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8318 (mm-40) REVERT: J 132 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8693 (t) REVERT: J 281 MET cc_start: 0.8822 (mtp) cc_final: 0.8438 (mtm) REVERT: K 5 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8515 (mptm) REVERT: K 46 GLU cc_start: 0.8528 (pt0) cc_final: 0.8258 (pm20) REVERT: K 97 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: K 217 ILE cc_start: 0.8272 (mt) cc_final: 0.8031 (mm) REVERT: K 288 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: K 292 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8729 (pp) REVERT: K 294 MET cc_start: 0.8643 (pmm) cc_final: 0.8367 (pmm) REVERT: K 314 SER cc_start: 0.7221 (OUTLIER) cc_final: 0.6779 (p) REVERT: L 13 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: L 14 ASP cc_start: 0.8415 (t0) cc_final: 0.7983 (t70) REVERT: L 103 SER cc_start: 0.8427 (m) cc_final: 0.7925 (p) REVERT: L 153 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7794 (tttm) REVERT: L 180 SER cc_start: 0.7807 (t) cc_final: 0.7545 (t) REVERT: L 267 GLU cc_start: 0.7677 (tp30) cc_final: 0.7219 (tp30) REVERT: L 278 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: L 288 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8347 (mp10) outliers start: 149 outliers final: 90 residues processed: 694 average time/residue: 1.3461 time to fit residues: 1092.2613 Evaluate side-chains 716 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 590 time to evaluate : 3.394 ------------------------------------------------------------------------------- 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 62 GLU 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 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 258 ILE 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 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 97 GLN 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 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 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 237 LEU 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 207 LEU 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 258 ILE 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 62 GLU 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 288 GLN 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 K residue 5 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 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 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 25 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 343 optimal weight: 0.8980 chunk 40 optimal weight: 0.0010 chunk 268 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.5344 ------------------------------------------------------------------------------- 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 K 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112183 restraints weight = 26724.032| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.68 r_work: 0.3030 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29076 Z= 0.091 Angle : 0.453 7.251 39396 Z= 0.241 Chirality : 0.046 0.163 4668 Planarity : 0.003 0.045 4992 Dihedral : 6.757 59.778 4287 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.66 % Allowed : 17.49 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3660 helix: 2.44 (0.14), residues: 1404 sheet: -0.66 (0.17), residues: 984 loop : -0.34 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.003 0.001 HIS E 304 PHE 0.010 0.001 PHE L 35 TYR 0.012 0.001 TYR E 146 ARG 0.008 0.000 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 1296) hydrogen bonds : angle 4.31200 ( 3600) covalent geometry : bond 0.00199 (29076) covalent geometry : angle 0.45250 (39396) *********************** 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 738 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 623 time to evaluate : 3.029 Fit side-chains REVERT: A 132 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8650 (t) REVERT: A 281 MET cc_start: 0.8782 (mtp) cc_final: 0.8411 (mtm) REVERT: B 14 ASP cc_start: 0.8108 (t0) cc_final: 0.7672 (t70) REVERT: B 52 ASP cc_start: 0.8649 (t0) cc_final: 0.8381 (t0) REVERT: B 62 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: B 288 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: C 248 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8063 (mt) REVERT: C 260 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7646 (mtt180) REVERT: C 294 MET cc_start: 0.8908 (pmm) cc_final: 0.8588 (pmm) REVERT: D 68 MET cc_start: 0.8610 (tpp) cc_final: 0.8362 (tpt) REVERT: D 78 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8302 (ttmt) REVERT: D 96 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8477 (mtt180) REVERT: D 97 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7307 (mp-120) REVERT: D 103 SER cc_start: 0.8423 (m) cc_final: 0.8097 (t) REVERT: D 217 ILE cc_start: 0.8252 (mt) cc_final: 0.7899 (mm) REVERT: D 245 TYR cc_start: 0.8496 (m-80) cc_final: 0.8284 (m-80) REVERT: D 267 GLU cc_start: 0.8215 (tp30) cc_final: 0.7739 (tp30) REVERT: D 292 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8567 (pp) REVERT: E 14 ASP cc_start: 0.8339 (t0) cc_final: 0.7913 (t70) REVERT: E 46 GLU cc_start: 0.8908 (pt0) cc_final: 0.8657 (pt0) REVERT: E 68 MET cc_start: 0.8794 (mmm) cc_final: 0.8499 (mmm) REVERT: E 153 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7791 (tttm) REVERT: E 180 SER cc_start: 0.7829 (t) cc_final: 0.7576 (t) REVERT: E 222 MET cc_start: 0.8558 (ptp) cc_final: 0.8122 (ptm) REVERT: E 248 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8141 (mt) REVERT: E 260 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7673 (mtm-85) REVERT: E 267 GLU cc_start: 0.7704 (tp30) cc_final: 0.7207 (tp30) REVERT: E 278 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: F 180 SER cc_start: 0.8194 (t) cc_final: 0.7909 (t) REVERT: F 247 ILE cc_start: 0.9002 (mt) cc_final: 0.8756 (mm) REVERT: F 278 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: F 288 GLN cc_start: 0.8447 (mt0) cc_final: 0.8128 (mt0) REVERT: F 292 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8762 (pp) REVERT: G 68 MET cc_start: 0.8611 (tpp) cc_final: 0.8353 (tpt) REVERT: G 78 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: G 267 GLU cc_start: 0.8263 (tp30) cc_final: 0.7777 (tp30) REVERT: G 292 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8529 (pp) REVERT: H 222 MET cc_start: 0.8548 (ptp) cc_final: 0.8276 (ptm) REVERT: H 248 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8051 (mt) REVERT: H 260 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7629 (mtt180) REVERT: H 294 MET cc_start: 0.8923 (pmm) cc_final: 0.8607 (pmm) REVERT: H 314 SER cc_start: 0.7218 (OUTLIER) cc_final: 0.6760 (p) REVERT: I 14 ASP cc_start: 0.8059 (t0) cc_final: 0.7796 (t70) REVERT: I 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8387 (t0) REVERT: I 62 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: J 132 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8631 (t) REVERT: J 222 MET cc_start: 0.8569 (ptp) cc_final: 0.8365 (ptp) REVERT: J 281 MET cc_start: 0.8771 (mtp) cc_final: 0.8390 (mtm) REVERT: K 5 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8524 (mptm) REVERT: K 21 ASP cc_start: 0.8296 (m-30) cc_final: 0.8060 (m-30) REVERT: K 180 SER cc_start: 0.8155 (t) cc_final: 0.7899 (t) REVERT: K 217 ILE cc_start: 0.8236 (mt) cc_final: 0.7929 (mm) REVERT: K 247 ILE cc_start: 0.9003 (mt) cc_final: 0.8770 (mm) REVERT: K 278 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: K 288 GLN cc_start: 0.8405 (mt0) cc_final: 0.8046 (mt0) REVERT: K 292 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8790 (pp) REVERT: K 294 MET cc_start: 0.8649 (pmm) cc_final: 0.8301 (pmm) REVERT: L 14 ASP cc_start: 0.8333 (t0) cc_final: 0.7925 (t70) REVERT: L 103 SER cc_start: 0.8416 (m) cc_final: 0.7884 (p) REVERT: L 153 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7758 (tttm) REVERT: L 180 SER cc_start: 0.7804 (t) cc_final: 0.7560 (t) REVERT: L 222 MET cc_start: 0.8583 (ptp) cc_final: 0.8122 (ptm) REVERT: L 248 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8162 (mt) REVERT: L 260 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7695 (mtm-85) REVERT: L 267 GLU cc_start: 0.7657 (tp30) cc_final: 0.7169 (tp30) REVERT: L 278 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: L 288 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8364 (mp10) outliers start: 115 outliers final: 70 residues processed: 706 average time/residue: 1.4155 time to fit residues: 1170.6466 Evaluate side-chains 697 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 604 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN 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 292 ILE 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 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 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 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 292 ILE Chi-restraints excluded: chain G residue 78 LYS 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 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 207 LEU 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 62 GLU 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 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 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 278 GLU Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 62 GLU 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 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 292 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 348 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 297 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 318 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 C 12 HIS D 263 ASN F 263 ASN G 277 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 = 0.3757 r_free = 0.3757 target = 0.156352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107445 restraints weight = 26398.156| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.72 r_work: 0.2961 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29076 Z= 0.177 Angle : 0.534 6.975 39396 Z= 0.284 Chirality : 0.048 0.172 4668 Planarity : 0.003 0.038 4992 Dihedral : 6.688 58.153 4282 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.72 % Allowed : 17.62 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3660 helix: 2.36 (0.14), residues: 1404 sheet: -0.67 (0.17), residues: 996 loop : -0.35 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 162 HIS 0.003 0.001 HIS J 193 PHE 0.016 0.002 PHE H 35 TYR 0.017 0.002 TYR E 146 ARG 0.008 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1296) hydrogen bonds : angle 4.39447 ( 3600) covalent geometry : bond 0.00412 (29076) covalent geometry : angle 0.53443 (39396) *********************** 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 722 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 605 time to evaluate : 2.926 Fit side-chains REVERT: A 132 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (t) REVERT: A 281 MET cc_start: 0.8818 (mtp) cc_final: 0.8441 (mtm) REVERT: B 14 ASP cc_start: 0.8243 (t0) cc_final: 0.7752 (t70) REVERT: B 52 ASP cc_start: 0.8678 (t0) cc_final: 0.8403 (t0) REVERT: B 288 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: C 205 MET cc_start: 0.6266 (ttt) cc_final: 0.5915 (ttp) REVERT: C 222 MET cc_start: 0.8612 (ptp) cc_final: 0.8317 (ptm) REVERT: C 248 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8176 (mt) REVERT: C 260 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7713 (mtt180) REVERT: C 294 MET cc_start: 0.8915 (pmm) cc_final: 0.8656 (pmm) REVERT: C 314 SER cc_start: 0.7340 (OUTLIER) cc_final: 0.6876 (p) REVERT: D 97 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: D 103 SER cc_start: 0.8547 (m) cc_final: 0.8185 (t) REVERT: D 217 ILE cc_start: 0.8256 (mt) cc_final: 0.7950 (mm) REVERT: D 245 TYR cc_start: 0.8517 (m-80) cc_final: 0.8246 (m-80) REVERT: D 267 GLU cc_start: 0.8249 (tp30) cc_final: 0.7751 (tp30) REVERT: D 292 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8537 (pp) REVERT: E 14 ASP cc_start: 0.8398 (t0) cc_final: 0.7967 (t70) REVERT: E 46 GLU cc_start: 0.8902 (pt0) cc_final: 0.8627 (pt0) REVERT: E 180 SER cc_start: 0.7785 (t) cc_final: 0.7528 (t) REVERT: E 222 MET cc_start: 0.8637 (ptp) cc_final: 0.8257 (ptm) REVERT: E 260 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7756 (mtm-85) REVERT: E 267 GLU cc_start: 0.7722 (tp30) cc_final: 0.7239 (tp30) REVERT: E 278 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: F 97 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: F 127 MET cc_start: 0.9174 (ttm) cc_final: 0.8819 (tpp) REVERT: F 180 SER cc_start: 0.8155 (t) cc_final: 0.7897 (t) REVERT: F 278 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: F 288 GLN cc_start: 0.8478 (mt0) cc_final: 0.8138 (mt0) REVERT: F 292 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8790 (pp) REVERT: F 314 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6660 (p) REVERT: G 78 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8272 (ttmt) REVERT: G 103 SER cc_start: 0.8543 (m) cc_final: 0.8168 (t) REVERT: G 217 ILE cc_start: 0.8285 (mt) cc_final: 0.7963 (mm) REVERT: G 245 TYR cc_start: 0.8580 (m-80) cc_final: 0.8366 (m-80) REVERT: G 267 GLU cc_start: 0.8338 (tp30) cc_final: 0.7861 (tp30) REVERT: G 292 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8534 (pp) REVERT: H 248 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8143 (mt) REVERT: H 260 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7673 (mtt180) REVERT: H 294 MET cc_start: 0.8928 (pmm) cc_final: 0.8670 (pmm) REVERT: H 314 SER cc_start: 0.7301 (OUTLIER) cc_final: 0.6832 (p) REVERT: I 14 ASP cc_start: 0.8166 (t0) cc_final: 0.7919 (t70) REVERT: I 62 GLU cc_start: 0.8224 (tp30) cc_final: 0.7965 (tp30) REVERT: I 102 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: I 267 GLU cc_start: 0.8115 (tp30) cc_final: 0.7746 (tp30) REVERT: I 288 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: I 314 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6798 (p) REVERT: J 132 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8687 (t) REVERT: J 281 MET cc_start: 0.8825 (mtp) cc_final: 0.8453 (mtm) REVERT: K 5 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (mptm) REVERT: K 97 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: K 180 SER cc_start: 0.8143 (t) cc_final: 0.7899 (t) REVERT: K 278 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: K 292 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8752 (pp) REVERT: K 294 MET cc_start: 0.8644 (pmm) cc_final: 0.8403 (pmm) REVERT: K 314 SER cc_start: 0.7152 (OUTLIER) cc_final: 0.6691 (p) REVERT: L 14 ASP cc_start: 0.8436 (t0) cc_final: 0.8006 (t70) REVERT: L 103 SER cc_start: 0.8401 (m) cc_final: 0.7898 (p) REVERT: L 153 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7815 (tttm) REVERT: L 180 SER cc_start: 0.7760 (t) cc_final: 0.7501 (t) REVERT: L 260 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7786 (mtm-85) REVERT: L 267 GLU cc_start: 0.7714 (tp30) cc_final: 0.7253 (tp30) REVERT: L 278 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: L 288 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8333 (mp10) outliers start: 117 outliers final: 78 residues processed: 693 average time/residue: 1.3757 time to fit residues: 1112.4925 Evaluate side-chains 697 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 593 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL 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 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 292 ILE Chi-restraints excluded: chain C residue 314 SER 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 E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 103 SER 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 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 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER 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 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU 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 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 207 LEU 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 102 LYS 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 288 GLN 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 278 GLU Chi-restraints excluded: chain K residue 5 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 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 36 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 183 optimal weight: 0.0470 chunk 136 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 63 optimal weight: 0.0060 chunk 140 optimal weight: 0.0770 chunk 195 optimal weight: 5.9990 chunk 288 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 252 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 overall best weight: 0.2452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 17 GLN B 97 GLN F 263 ASN J 97 GLN J 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113977 restraints weight = 26695.894| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.67 r_work: 0.3056 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29076 Z= 0.084 Angle : 0.449 7.762 39396 Z= 0.239 Chirality : 0.046 0.162 4668 Planarity : 0.003 0.042 4992 Dihedral : 6.179 59.828 4279 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.05 % Allowed : 18.35 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3660 helix: 2.50 (0.14), residues: 1404 sheet: -0.71 (0.16), residues: 984 loop : -0.34 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.004 0.000 HIS F 193 PHE 0.013 0.001 PHE C 35 TYR 0.011 0.001 TYR A 311 ARG 0.010 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 1296) hydrogen bonds : angle 4.26651 ( 3600) covalent geometry : bond 0.00184 (29076) covalent geometry : angle 0.44920 (39396) ********************** 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 718 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 622 time to evaluate : 3.019 Fit side-chains REVERT: A 103 SER cc_start: 0.8277 (m) cc_final: 0.7793 (p) REVERT: A 132 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8635 (t) REVERT: A 260 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: A 281 MET cc_start: 0.8794 (mtp) cc_final: 0.8413 (mtm) REVERT: B 14 ASP cc_start: 0.8105 (t0) cc_final: 0.7662 (t70) REVERT: B 52 ASP cc_start: 0.8638 (t0) cc_final: 0.8391 (t0) REVERT: B 62 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: B 288 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: C 181 ILE cc_start: 0.7650 (mt) cc_final: 0.7336 (mm) REVERT: C 222 MET cc_start: 0.8514 (ptp) cc_final: 0.8220 (ptm) REVERT: C 248 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8078 (mt) REVERT: C 260 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7643 (mtt180) REVERT: C 294 MET cc_start: 0.8893 (pmm) cc_final: 0.8592 (pmm) REVERT: D 103 SER cc_start: 0.8428 (m) cc_final: 0.8098 (t) REVERT: D 267 GLU cc_start: 0.8195 (tp30) cc_final: 0.7776 (tp30) REVERT: E 14 ASP cc_start: 0.8379 (t0) cc_final: 0.7957 (t70) REVERT: E 46 GLU cc_start: 0.8849 (pt0) cc_final: 0.8605 (pt0) REVERT: E 68 MET cc_start: 0.8747 (mmm) cc_final: 0.8476 (mmm) REVERT: E 97 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8374 (mm-40) REVERT: E 180 SER cc_start: 0.7697 (t) cc_final: 0.7457 (t) REVERT: E 222 MET cc_start: 0.8540 (ptp) cc_final: 0.8228 (ptp) REVERT: E 260 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7685 (mtm-85) REVERT: E 267 GLU cc_start: 0.7702 (tp30) cc_final: 0.7204 (tp30) REVERT: E 278 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: E 288 GLN cc_start: 0.8717 (mt0) cc_final: 0.8278 (mp10) REVERT: F 180 SER cc_start: 0.8267 (t) cc_final: 0.7988 (t) REVERT: F 278 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: F 288 GLN cc_start: 0.8468 (mt0) cc_final: 0.8119 (mt0) REVERT: F 292 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8706 (pp) REVERT: G 21 ASP cc_start: 0.8272 (m-30) cc_final: 0.8004 (m-30) REVERT: G 78 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8295 (ttmt) REVERT: G 103 SER cc_start: 0.8429 (m) cc_final: 0.8092 (t) REVERT: G 267 GLU cc_start: 0.8262 (tp30) cc_final: 0.7806 (tp30) REVERT: H 148 GLU cc_start: 0.8157 (tt0) cc_final: 0.7779 (tt0) REVERT: H 222 MET cc_start: 0.8549 (ptp) cc_final: 0.8332 (ptm) REVERT: H 248 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8061 (mt) REVERT: H 260 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7676 (mtt180) REVERT: H 294 MET cc_start: 0.8907 (pmm) cc_final: 0.8610 (pmm) REVERT: H 314 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6717 (p) REVERT: I 14 ASP cc_start: 0.8021 (t0) cc_final: 0.7780 (t70) REVERT: I 62 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: I 267 GLU cc_start: 0.7955 (tp30) cc_final: 0.7586 (tp30) REVERT: J 132 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8615 (t) REVERT: J 260 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: J 281 MET cc_start: 0.8773 (mtp) cc_final: 0.8398 (mtm) REVERT: K 5 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8503 (mptm) REVERT: K 79 ILE cc_start: 0.8840 (pt) cc_final: 0.8627 (mm) REVERT: K 180 SER cc_start: 0.8232 (t) cc_final: 0.7972 (t) REVERT: K 247 ILE cc_start: 0.8914 (mt) cc_final: 0.8708 (mm) REVERT: K 278 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: K 288 GLN cc_start: 0.8376 (mt0) cc_final: 0.8069 (mt0) REVERT: K 292 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8770 (pp) REVERT: K 294 MET cc_start: 0.8618 (pmm) cc_final: 0.8345 (pmm) REVERT: L 14 ASP cc_start: 0.8380 (t0) cc_final: 0.7973 (t70) REVERT: L 68 MET cc_start: 0.8783 (mmm) cc_final: 0.8557 (mmm) REVERT: L 103 SER cc_start: 0.8403 (m) cc_final: 0.7896 (p) REVERT: L 153 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7751 (tttm) REVERT: L 180 SER cc_start: 0.7659 (t) cc_final: 0.7415 (t) REVERT: L 260 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7717 (mtm-85) REVERT: L 267 GLU cc_start: 0.7638 (tp30) cc_final: 0.7145 (tp30) REVERT: L 278 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6936 (pm20) REVERT: L 288 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8370 (mp10) outliers start: 96 outliers final: 54 residues processed: 692 average time/residue: 1.4444 time to fit residues: 1169.0618 Evaluate side-chains 669 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 597 time to evaluate : 3.251 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 62 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 285 SER Chi-restraints excluded: chain B residue 288 GLN 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 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 292 ILE 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 E residue 62 GLU Chi-restraints excluded: chain E residue 97 GLN 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 278 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU 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 62 GLU 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 285 SER Chi-restraints excluded: chain J residue 12 HIS 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 278 GLU Chi-restraints excluded: chain K residue 5 LYS 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 292 ILE 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 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 140 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 294 optimal weight: 0.1980 chunk 232 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 356 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 J 97 GLN J 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108976 restraints weight = 26702.674| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.60 r_work: 0.2978 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2833 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= 0.116 Angle : 0.482 7.539 39396 Z= 0.254 Chirality : 0.046 0.166 4668 Planarity : 0.003 0.042 4992 Dihedral : 5.838 59.628 4272 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.83 % Allowed : 18.58 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3660 helix: 2.51 (0.14), residues: 1404 sheet: -0.73 (0.17), residues: 948 loop : -0.39 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 162 HIS 0.003 0.001 HIS A 193 PHE 0.013 0.001 PHE L 35 TYR 0.011 0.001 TYR G 311 ARG 0.009 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1296) hydrogen bonds : angle 4.25467 ( 3600) covalent geometry : bond 0.00264 (29076) covalent geometry : angle 0.48168 (39396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29750.78 seconds wall clock time: 511 minutes 4.52 seconds (30664.52 seconds total)