Starting phenix.real_space_refine on Tue Jun 24 11:45:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbm_27290/06_2025/8dbm_27290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbm_27290/06_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_27290/06_2025/8dbm_27290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbm_27290/06_2025/8dbm_27290.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbm_27290/06_2025/8dbm_27290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbm_27290/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.66, per 1000 atoms: 0.58 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: 7.10 Conformation dependent library (CDL) restraints added in 4.0 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: 3.78 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: 11.00 Time building geometry restraints manager: 8.33 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: 0.26 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.220 Check model and map are aligned: 0.180 Set scattering table: 0.280 Process input model: 65.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.750 ------------------------------------------------------------------------------- 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 : 3.037 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: 1.4683 time to fit residues: 1528.5899 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 : 4.428 ------------------------------------------------------------------------------- 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 = 26197.916| |-----------------------------------------------------------------------------| 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 : 3.187 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: 0.7866 (p) REVERT: A 128 ASP cc_start: 0.8896 (m-30) cc_final: 0.8673 (m-30) REVERT: A 180 SER cc_start: 0.7850 (t) cc_final: 0.7457 (t) REVERT: A 248 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 260 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7825 (mtt180) REVERT: A 281 MET cc_start: 0.8778 (mtp) cc_final: 0.8408 (mtm) REVERT: B 14 ASP cc_start: 0.8273 (t0) cc_final: 0.7847 (t70) REVERT: B 52 ASP cc_start: 0.8829 (t0) cc_final: 0.8589 (t0) REVERT: B 191 LEU cc_start: 0.6931 (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: 0.8715 (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: 0.8067 (mt) REVERT: C 260 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7739 (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: 0.8161 (mt0) REVERT: C 294 MET cc_start: 0.8922 (pmm) cc_final: 0.8639 (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: 0.7572 (m110) REVERT: D 261 ILE cc_start: 0.8396 (mt) cc_final: 0.8111 (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: 0.8726 (pt0) REVERT: E 103 SER cc_start: 0.8493 (m) cc_final: 0.8045 (p) REVERT: E 180 SER cc_start: 0.7830 (t) cc_final: 0.7501 (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: 0.7368 (tp30) REVERT: E 282 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8261 (mmtp) REVERT: F 97 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: F 180 SER cc_start: 0.8298 (t) cc_final: 0.8069 (t) REVERT: F 259 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8090 (p) REVERT: F 261 ILE cc_start: 0.8528 (mt) cc_final: 0.8273 (mm) REVERT: F 294 MET cc_start: 0.8811 (pmm) cc_final: 0.8434 (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: 0.8146 (m-40) cc_final: 0.7626 (m110) REVERT: G 261 ILE cc_start: 0.8369 (mt) cc_final: 0.8113 (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: 0.8478 (OUTLIER) cc_final: 0.8092 (mt) REVERT: H 260 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7736 (mtm-85) REVERT: H 281 MET cc_start: 0.8684 (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: 0.8929 (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: 0.7390 (mp10) REVERT: I 191 LEU cc_start: 0.6921 (mp) cc_final: 0.5917 (tt) REVERT: I 288 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: J 5 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8759 (mmmt) REVERT: J 103 SER cc_start: 0.8302 (m) cc_final: 0.7852 (p) REVERT: J 128 ASP cc_start: 0.8893 (m-30) cc_final: 0.8671 (m-30) REVERT: J 180 SER cc_start: 0.7916 (t) cc_final: 0.7522 (t) REVERT: J 248 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8285 (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: 0.8388 (mtm) REVERT: K 97 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: K 180 SER cc_start: 0.8266 (t) cc_final: 0.8044 (t) REVERT: K 217 ILE cc_start: 0.8228 (mt) cc_final: 0.7993 (mm) REVERT: K 259 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8087 (p) REVERT: K 261 ILE cc_start: 0.8491 (mt) cc_final: 0.8259 (mm) REVERT: K 294 MET cc_start: 0.8785 (pmm) cc_final: 0.8402 (pmm) REVERT: L 14 ASP cc_start: 0.8453 (t0) cc_final: 0.8055 (t70) REVERT: L 35 PHE cc_start: 0.8544 (m-80) cc_final: 0.8304 (m-80) REVERT: L 103 SER cc_start: 0.8505 (m) cc_final: 0.8057 (p) REVERT: L 180 SER cc_start: 0.7829 (t) cc_final: 0.7493 (t) REVERT: L 260 ARG cc_start: 0.8297 (mtt180) cc_final: 0.8066 (mtt180) REVERT: L 267 GLU cc_start: 0.7793 (tp30) cc_final: 0.7392 (tp30) outliers start: 165 outliers final: 90 residues processed: 768 average time/residue: 1.7707 time to fit residues: 1576.2334 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 : 3.256 ------------------------------------------------------------------------------- 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: 3.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 332 optimal weight: 0.0670 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: 0.4980 chunk 338 optimal weight: 4.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- 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 C 97 GLN D 130 HIS D 263 ASN E 130 HIS F 130 HIS F 263 ASN F 305 ASN G 130 HIS G 263 ASN H 97 GLN J 97 GLN K 130 HIS K 263 ASN L 130 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109069 restraints weight = 26144.008| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.59 r_work: 0.2992 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29076 Z= 0.150 Angle : 0.511 6.393 39396 Z= 0.276 Chirality : 0.048 0.173 4668 Planarity : 0.003 0.026 4992 Dihedral : 8.188 59.972 4310 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.03 % Allowed : 14.66 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.14), residues: 3660 helix: 2.14 (0.14), residues: 1404 sheet: -0.43 (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 J 162 HIS 0.004 0.001 HIS D 12 PHE 0.012 0.002 PHE D 138 TYR 0.015 0.002 TYR L 146 ARG 0.006 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1296) hydrogen bonds : angle 4.58381 ( 3600) covalent geometry : bond 0.00342 (29076) covalent geometry : angle 0.51091 (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 792 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 634 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: A 97 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: A 103 SER cc_start: 0.8278 (m) cc_final: 0.7860 (p) REVERT: A 132 SER cc_start: 0.8911 (p) cc_final: 0.8668 (t) REVERT: A 180 SER cc_start: 0.7850 (t) cc_final: 0.7476 (t) REVERT: A 248 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 260 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7743 (mtt180) REVERT: A 281 MET cc_start: 0.8846 (mtp) cc_final: 0.8461 (mtm) REVERT: B 14 ASP cc_start: 0.8220 (t0) cc_final: 0.7767 (t70) REVERT: B 52 ASP cc_start: 0.8763 (t0) cc_final: 0.8522 (t0) REVERT: B 62 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7833 (tp30) REVERT: B 191 LEU cc_start: 0.6870 (mp) cc_final: 0.6083 (tt) REVERT: B 288 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: C 5 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8652 (mmmt) REVERT: C 35 PHE cc_start: 0.8427 (m-80) cc_final: 0.8186 (m-80) REVERT: C 128 ASP cc_start: 0.8901 (m-30) cc_final: 0.8660 (m-30) REVERT: C 260 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7663 (mtt180) REVERT: C 281 MET cc_start: 0.8662 (mtp) cc_final: 0.8118 (mtm) REVERT: C 288 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: C 294 MET cc_start: 0.8922 (pmm) cc_final: 0.8576 (pmm) REVERT: D 78 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8286 (ttmt) REVERT: D 97 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: D 103 SER cc_start: 0.8335 (m) cc_final: 0.8018 (t) REVERT: D 245 TYR cc_start: 0.8557 (m-80) cc_final: 0.8233 (m-80) REVERT: D 261 ILE cc_start: 0.8385 (mt) cc_final: 0.8128 (mm) REVERT: E 13 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: E 14 ASP cc_start: 0.8391 (t0) cc_final: 0.8004 (t70) REVERT: E 46 GLU cc_start: 0.8880 (pt0) cc_final: 0.8593 (pt0) REVERT: E 103 SER cc_start: 0.8580 (m) cc_final: 0.8121 (p) REVERT: E 180 SER cc_start: 0.7894 (t) cc_final: 0.7588 (t) REVERT: E 222 MET cc_start: 0.8500 (ptp) cc_final: 0.8154 (ptm) REVERT: E 267 GLU cc_start: 0.7768 (tp30) cc_final: 0.7312 (tp30) REVERT: F 97 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: F 180 SER cc_start: 0.8275 (t) cc_final: 0.7981 (t) REVERT: F 288 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: F 294 MET cc_start: 0.8722 (pmm) cc_final: 0.8375 (pmm) REVERT: F 314 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.6872 (p) REVERT: G 78 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8287 (ttmt) REVERT: G 97 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: G 103 SER cc_start: 0.8310 (m) cc_final: 0.7995 (t) REVERT: G 245 TYR cc_start: 0.8562 (m-80) cc_final: 0.8224 (m-80) REVERT: G 261 ILE cc_start: 0.8366 (mt) cc_final: 0.8130 (mm) REVERT: H 5 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8684 (mmmt) REVERT: H 13 GLN cc_start: 0.8510 (tp40) cc_final: 0.8245 (mm-40) REVERT: H 35 PHE cc_start: 0.8443 (m-80) cc_final: 0.8236 (m-80) REVERT: H 115 MET cc_start: 0.9083 (mtp) cc_final: 0.8817 (mtp) REVERT: H 128 ASP cc_start: 0.8894 (m-30) cc_final: 0.8656 (m-30) REVERT: H 260 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7640 (mtt180) REVERT: H 288 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: H 294 MET cc_start: 0.8919 (pmm) cc_final: 0.8571 (pmm) REVERT: I 14 ASP cc_start: 0.8187 (t0) cc_final: 0.7926 (t70) REVERT: I 52 ASP cc_start: 0.8746 (t0) cc_final: 0.8513 (t0) REVERT: I 191 LEU cc_start: 0.7023 (mp) cc_final: 0.5987 (tt) REVERT: J 13 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: J 103 SER cc_start: 0.8247 (m) cc_final: 0.7822 (p) REVERT: J 132 SER cc_start: 0.8917 (p) cc_final: 0.8656 (t) REVERT: J 180 SER cc_start: 0.7960 (t) cc_final: 0.7593 (t) REVERT: J 248 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8270 (mt) REVERT: J 260 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7763 (mtt180) REVERT: J 281 MET cc_start: 0.8826 (mtp) cc_final: 0.8440 (mtm) REVERT: K 97 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: K 180 SER cc_start: 0.8224 (t) cc_final: 0.7930 (t) REVERT: K 217 ILE cc_start: 0.8406 (mt) cc_final: 0.8103 (mm) REVERT: K 288 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: K 314 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.6926 (p) REVERT: L 13 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: L 14 ASP cc_start: 0.8436 (t0) cc_final: 0.8051 (t70) REVERT: L 35 PHE cc_start: 0.8534 (m-80) cc_final: 0.8283 (m-80) REVERT: L 103 SER cc_start: 0.8575 (m) cc_final: 0.8115 (p) REVERT: L 180 SER cc_start: 0.7897 (t) cc_final: 0.7596 (t) REVERT: L 267 GLU cc_start: 0.7764 (tp30) cc_final: 0.7309 (tp30) REVERT: L 314 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6996 (p) outliers start: 158 outliers final: 88 residues processed: 738 average time/residue: 1.5062 time to fit residues: 1287.0685 Evaluate side-chains 715 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 603 time to evaluate : 3.621 ------------------------------------------------------------------------------- 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 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 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 97 GLN 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 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 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 176 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 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 292 ILE Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 62 GLU 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 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 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 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 176 LYS Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 280 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 97 GLN D 263 ASN E 130 HIS F 263 ASN H 97 GLN K 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.158536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111042 restraints weight = 26486.624| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.59 r_work: 0.3016 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 29076 Z= 0.104 Angle : 0.460 6.582 39396 Z= 0.248 Chirality : 0.046 0.166 4668 Planarity : 0.003 0.029 4992 Dihedral : 7.549 58.883 4298 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.48 % Allowed : 15.62 % Favored : 79.90 % 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: 0.94 (0.14), residues: 3660 helix: 2.25 (0.14), residues: 1404 sheet: -0.46 (0.17), residues: 996 loop : -0.21 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.004 0.001 HIS D 12 PHE 0.011 0.001 PHE D 35 TYR 0.012 0.001 TYR L 146 ARG 0.006 0.000 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 1296) hydrogen bonds : angle 4.46641 ( 3600) covalent geometry : bond 0.00228 (29076) covalent geometry : angle 0.45986 (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 767 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 626 time to evaluate : 3.300 Fit side-chains REVERT: A 97 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: A 132 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8686 (t) REVERT: A 180 SER cc_start: 0.7867 (t) cc_final: 0.7507 (t) REVERT: A 248 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 260 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7732 (mtt180) REVERT: A 281 MET cc_start: 0.8818 (mtp) cc_final: 0.8431 (mtm) REVERT: A 288 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: B 14 ASP cc_start: 0.8163 (t0) cc_final: 0.7704 (t70) REVERT: B 52 ASP cc_start: 0.8737 (t0) cc_final: 0.8484 (t0) REVERT: B 62 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: B 79 ILE cc_start: 0.8900 (pt) cc_final: 0.8683 (mm) REVERT: B 191 LEU cc_start: 0.6739 (mp) cc_final: 0.5979 (tt) REVERT: B 267 GLU cc_start: 0.8044 (tp30) cc_final: 0.7843 (tp30) REVERT: C 22 ARG cc_start: 0.8881 (mtt90) cc_final: 0.8623 (mtt90) REVERT: C 115 MET cc_start: 0.9082 (mtp) cc_final: 0.8831 (mtp) REVERT: C 248 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 260 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7524 (mtt90) REVERT: C 281 MET cc_start: 0.8617 (mtp) cc_final: 0.8141 (mtm) REVERT: C 294 MET cc_start: 0.8917 (pmm) cc_final: 0.8629 (pmm) REVERT: D 68 MET cc_start: 0.8702 (tpp) cc_final: 0.8441 (tpt) REVERT: D 78 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8282 (ttmt) REVERT: D 103 SER cc_start: 0.8367 (m) cc_final: 0.8049 (t) REVERT: D 245 TYR cc_start: 0.8514 (m-80) cc_final: 0.8163 (m-80) REVERT: D 261 ILE cc_start: 0.8356 (mt) cc_final: 0.8130 (mm) REVERT: D 267 GLU cc_start: 0.8232 (tp30) cc_final: 0.7815 (tp30) REVERT: D 292 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8568 (pp) REVERT: E 14 ASP cc_start: 0.8385 (t0) cc_final: 0.7987 (t70) REVERT: E 46 GLU cc_start: 0.8891 (pt0) cc_final: 0.8625 (pt0) REVERT: E 103 SER cc_start: 0.8544 (m) cc_final: 0.8333 (t) REVERT: E 153 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7725 (tttm) REVERT: E 180 SER cc_start: 0.7849 (t) cc_final: 0.7567 (t) REVERT: E 222 MET cc_start: 0.8516 (ptp) cc_final: 0.8212 (ptm) REVERT: E 248 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8184 (mt) REVERT: E 267 GLU cc_start: 0.7746 (tp30) cc_final: 0.7260 (tp30) REVERT: F 180 SER cc_start: 0.8215 (t) cc_final: 0.7949 (t) REVERT: F 288 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: F 292 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8744 (pp) REVERT: F 294 MET cc_start: 0.8740 (pmm) cc_final: 0.8358 (pmm) REVERT: G 78 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8299 (ttmt) REVERT: G 103 SER cc_start: 0.8349 (m) cc_final: 0.8039 (t) REVERT: G 245 TYR cc_start: 0.8482 (m-80) cc_final: 0.8141 (m-80) REVERT: G 261 ILE cc_start: 0.8316 (mt) cc_final: 0.8097 (mm) REVERT: G 267 GLU cc_start: 0.8260 (tp30) cc_final: 0.7835 (tp30) REVERT: G 292 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8565 (pp) REVERT: H 35 PHE cc_start: 0.8480 (m-80) cc_final: 0.8251 (m-80) REVERT: H 248 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8021 (mt) REVERT: H 260 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7484 (mtt90) REVERT: H 294 MET cc_start: 0.8903 (pmm) cc_final: 0.8656 (pmm) REVERT: I 14 ASP cc_start: 0.8112 (t0) cc_final: 0.7841 (t70) REVERT: I 52 ASP cc_start: 0.8722 (t0) cc_final: 0.8472 (t0) REVERT: I 79 ILE cc_start: 0.8894 (pt) cc_final: 0.8677 (mm) REVERT: I 191 LEU cc_start: 0.6668 (mp) cc_final: 0.5952 (tt) REVERT: I 267 GLU cc_start: 0.8073 (tp30) cc_final: 0.7860 (tp30) REVERT: J 132 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8629 (t) REVERT: J 180 SER cc_start: 0.7916 (t) cc_final: 0.7603 (t) REVERT: J 248 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8135 (mt) REVERT: J 260 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7738 (mtt180) REVERT: J 281 MET cc_start: 0.8807 (mtp) cc_final: 0.8427 (mtm) REVERT: J 288 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: K 180 SER cc_start: 0.8180 (t) cc_final: 0.7916 (t) REVERT: K 217 ILE cc_start: 0.8347 (mt) cc_final: 0.7745 (mm) REVERT: K 288 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: K 292 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8783 (pp) REVERT: L 14 ASP cc_start: 0.8396 (t0) cc_final: 0.8008 (t70) REVERT: L 68 MET cc_start: 0.8807 (mmm) cc_final: 0.8605 (mmm) REVERT: L 103 SER cc_start: 0.8551 (m) cc_final: 0.8316 (t) REVERT: L 180 SER cc_start: 0.7864 (t) cc_final: 0.7588 (t) REVERT: L 248 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8199 (mt) REVERT: L 267 GLU cc_start: 0.7725 (tp30) cc_final: 0.7248 (tp30) outliers start: 141 outliers final: 81 residues processed: 719 average time/residue: 1.6267 time to fit residues: 1372.0085 Evaluate side-chains 708 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 607 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain 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 292 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU 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 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 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 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 292 ILE Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain 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 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 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 229 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 D 277 GLN F 263 ASN G 277 GLN I 135 GLN J 97 GLN K 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108084 restraints weight = 26395.657| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.71 r_work: 0.2972 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29076 Z= 0.148 Angle : 0.505 6.630 39396 Z= 0.270 Chirality : 0.047 0.172 4668 Planarity : 0.003 0.031 4992 Dihedral : 7.217 59.389 4290 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.48 % Allowed : 15.81 % Favored : 79.71 % 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: 0.94 (0.14), residues: 3660 helix: 2.32 (0.14), residues: 1404 sheet: -0.51 (0.17), residues: 996 loop : -0.25 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP J 162 HIS 0.003 0.001 HIS H 193 PHE 0.012 0.001 PHE D 138 TYR 0.014 0.002 TYR L 146 ARG 0.006 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1296) hydrogen bonds : angle 4.43439 ( 3600) covalent geometry : bond 0.00339 (29076) covalent geometry : angle 0.50463 (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 747 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 606 time to evaluate : 3.196 Fit side-chains REVERT: A 97 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8283 (mm-40) REVERT: A 132 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8705 (t) REVERT: A 248 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8153 (mt) REVERT: A 260 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7735 (mtt180) REVERT: A 281 MET cc_start: 0.8837 (mtp) cc_final: 0.8439 (mtm) REVERT: A 288 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: B 14 ASP cc_start: 0.8255 (t0) cc_final: 0.7800 (t70) REVERT: B 52 ASP cc_start: 0.8742 (t0) cc_final: 0.8503 (t0) REVERT: B 97 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: B 267 GLU cc_start: 0.8124 (tp30) cc_final: 0.7912 (tp30) REVERT: B 314 SER cc_start: 0.7279 (OUTLIER) cc_final: 0.6992 (p) REVERT: C 115 MET cc_start: 0.9182 (mtp) cc_final: 0.8900 (mtp) REVERT: C 260 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7675 (mtt180) REVERT: C 294 MET cc_start: 0.8946 (pmm) cc_final: 0.8692 (pmm) REVERT: D 22 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.8197 (mtt90) REVERT: D 78 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8281 (ttmt) REVERT: D 103 SER cc_start: 0.8407 (m) cc_final: 0.8069 (t) REVERT: D 217 ILE cc_start: 0.8259 (mt) cc_final: 0.7956 (mm) REVERT: D 245 TYR cc_start: 0.8538 (m-80) cc_final: 0.8217 (m-80) REVERT: D 261 ILE cc_start: 0.8419 (mt) cc_final: 0.8145 (mm) REVERT: D 267 GLU cc_start: 0.8246 (tp30) cc_final: 0.7831 (tp30) REVERT: D 292 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8545 (pp) REVERT: E 13 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: E 14 ASP cc_start: 0.8394 (t0) cc_final: 0.7990 (t70) REVERT: E 46 GLU cc_start: 0.8876 (pt0) cc_final: 0.8572 (pt0) REVERT: E 103 SER cc_start: 0.8486 (m) cc_final: 0.8021 (p) REVERT: E 153 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7804 (tttm) REVERT: E 180 SER cc_start: 0.7877 (t) cc_final: 0.7611 (t) REVERT: E 260 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7721 (mtm-85) REVERT: E 267 GLU cc_start: 0.7754 (tp30) cc_final: 0.7263 (tp30) REVERT: E 314 SER cc_start: 0.7153 (OUTLIER) cc_final: 0.6915 (p) REVERT: F 97 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: F 180 SER cc_start: 0.8226 (t) cc_final: 0.7970 (t) REVERT: F 288 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: F 292 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8738 (pp) REVERT: F 294 MET cc_start: 0.8727 (pmm) cc_final: 0.8356 (pmm) REVERT: F 314 SER cc_start: 0.7151 (OUTLIER) cc_final: 0.6726 (p) REVERT: G 78 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: G 103 SER cc_start: 0.8392 (m) cc_final: 0.8052 (t) REVERT: G 245 TYR cc_start: 0.8508 (m-80) cc_final: 0.8192 (m-80) REVERT: G 261 ILE cc_start: 0.8373 (mt) cc_final: 0.8109 (mm) REVERT: G 267 GLU cc_start: 0.8272 (tp30) cc_final: 0.7843 (tp30) REVERT: G 292 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8534 (pp) REVERT: H 35 PHE cc_start: 0.8467 (m-80) cc_final: 0.8207 (m-80) REVERT: H 260 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7647 (mtt180) REVERT: H 294 MET cc_start: 0.8944 (pmm) cc_final: 0.8647 (pmm) REVERT: I 14 ASP cc_start: 0.8218 (t0) cc_final: 0.7930 (t70) REVERT: I 52 ASP cc_start: 0.8713 (t0) cc_final: 0.8453 (t0) REVERT: I 97 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: I 267 GLU cc_start: 0.8164 (tp30) cc_final: 0.7941 (tp30) REVERT: I 314 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6923 (p) REVERT: J 13 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: J 132 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8671 (t) REVERT: J 180 SER cc_start: 0.7886 (t) cc_final: 0.7610 (t) REVERT: J 248 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8242 (mt) REVERT: J 260 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7745 (mtt180) REVERT: J 281 MET cc_start: 0.8835 (mtp) cc_final: 0.8441 (mtm) REVERT: J 288 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: K 180 SER cc_start: 0.8181 (t) cc_final: 0.7948 (t) REVERT: K 288 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: K 292 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8782 (pp) REVERT: K 294 MET cc_start: 0.8646 (pmm) cc_final: 0.8398 (pmm) REVERT: K 314 SER cc_start: 0.7181 (OUTLIER) cc_final: 0.6736 (p) REVERT: L 14 ASP cc_start: 0.8419 (t0) cc_final: 0.8014 (t70) REVERT: L 153 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7781 (tttm) REVERT: L 180 SER cc_start: 0.7866 (t) cc_final: 0.7613 (t) REVERT: L 260 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7727 (mtm-85) REVERT: L 267 GLU cc_start: 0.7750 (tp30) cc_final: 0.7274 (tp30) REVERT: L 278 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: L 288 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: L 314 SER cc_start: 0.7129 (OUTLIER) cc_final: 0.6918 (p) outliers start: 141 outliers final: 82 residues processed: 702 average time/residue: 1.5407 time to fit residues: 1254.7404 Evaluate side-chains 705 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 595 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 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 63 ILE Chi-restraints excluded: chain D residue 78 LYS 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 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 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 314 SER 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 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 K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 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 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 288 GLN Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 77 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 342 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 C 97 GLN F 135 GLN F 263 ASN H 12 HIS J 97 GLN K 135 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 = 0.3744 r_free = 0.3744 target = 0.155103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103972 restraints weight = 26354.728| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.61 r_work: 0.2924 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29076 Z= 0.210 Angle : 0.561 6.670 39396 Z= 0.300 Chirality : 0.049 0.180 4668 Planarity : 0.003 0.032 4992 Dihedral : 7.307 55.557 4290 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.18 % Allowed : 15.30 % Favored : 79.52 % 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: 0.82 (0.14), residues: 3660 helix: 2.23 (0.14), residues: 1404 sheet: -0.60 (0.17), residues: 996 loop : -0.31 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 162 HIS 0.004 0.001 HIS E 123 PHE 0.015 0.002 PHE D 138 TYR 0.018 0.002 TYR L 146 ARG 0.005 0.001 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 1296) hydrogen bonds : angle 4.50387 ( 3600) covalent geometry : bond 0.00491 (29076) covalent geometry : angle 0.56077 (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 770 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 607 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8314 (m) cc_final: 0.7732 (p) REVERT: A 132 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8730 (t) REVERT: A 248 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 281 MET cc_start: 0.8806 (mtp) cc_final: 0.8373 (mtm) REVERT: A 288 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: B 14 ASP cc_start: 0.8274 (t0) cc_final: 0.7799 (t70) REVERT: B 52 ASP cc_start: 0.8694 (t0) cc_final: 0.8423 (t0) REVERT: B 62 GLU cc_start: 0.8227 (tp30) cc_final: 0.7980 (tp30) REVERT: B 314 SER cc_start: 0.7312 (OUTLIER) cc_final: 0.7026 (p) REVERT: C 115 MET cc_start: 0.9236 (mtp) cc_final: 0.8952 (mtp) REVERT: C 260 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7718 (mtt180) REVERT: C 294 MET cc_start: 0.8942 (pmm) cc_final: 0.8683 (pmm) REVERT: C 314 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.7046 (p) REVERT: D 37 ASN cc_start: 0.8496 (p0) cc_final: 0.8282 (p0) REVERT: D 68 MET cc_start: 0.8723 (tpp) cc_final: 0.8447 (tpt) REVERT: D 78 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8286 (ttmt) REVERT: D 97 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: D 103 SER cc_start: 0.8507 (m) cc_final: 0.8136 (t) REVERT: D 217 ILE cc_start: 0.8325 (mt) cc_final: 0.7991 (mm) REVERT: D 245 TYR cc_start: 0.8552 (m-80) cc_final: 0.8267 (m-80) REVERT: D 261 ILE cc_start: 0.8412 (mt) cc_final: 0.8151 (mm) REVERT: D 267 GLU cc_start: 0.8272 (tp30) cc_final: 0.7777 (tp30) REVERT: D 292 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8521 (pp) REVERT: E 13 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: E 14 ASP cc_start: 0.8423 (t0) cc_final: 0.8012 (t70) REVERT: E 46 GLU cc_start: 0.8925 (pt0) cc_final: 0.8633 (pt0) REVERT: E 103 SER cc_start: 0.8426 (m) cc_final: 0.7911 (p) REVERT: E 153 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7835 (tttm) REVERT: E 180 SER cc_start: 0.7794 (t) cc_final: 0.7507 (t) REVERT: E 248 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8227 (mt) REVERT: E 267 GLU cc_start: 0.7694 (tp30) cc_final: 0.7241 (tp30) REVERT: E 278 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: F 97 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: F 180 SER cc_start: 0.8189 (t) cc_final: 0.7910 (t) REVERT: F 292 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8733 (pp) REVERT: F 294 MET cc_start: 0.8709 (pmm) cc_final: 0.8347 (pmm) REVERT: F 314 SER cc_start: 0.7235 (OUTLIER) cc_final: 0.6803 (p) REVERT: G 14 ASP cc_start: 0.8175 (t70) cc_final: 0.7932 (t70) REVERT: G 37 ASN cc_start: 0.8465 (p0) cc_final: 0.8237 (p0) REVERT: G 78 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: G 97 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: G 217 ILE cc_start: 0.8296 (mt) cc_final: 0.7949 (mm) REVERT: G 245 TYR cc_start: 0.8544 (m-80) cc_final: 0.8244 (m-80) REVERT: G 261 ILE cc_start: 0.8402 (mt) cc_final: 0.8157 (mm) REVERT: G 267 GLU cc_start: 0.8328 (tp30) cc_final: 0.7818 (tp30) REVERT: G 292 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8514 (pp) REVERT: H 35 PHE cc_start: 0.8469 (m-80) cc_final: 0.8199 (m-80) REVERT: H 260 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7638 (mtm-85) REVERT: H 294 MET cc_start: 0.8933 (pmm) cc_final: 0.8684 (pmm) REVERT: I 14 ASP cc_start: 0.8243 (t0) cc_final: 0.7994 (t70) REVERT: I 52 ASP cc_start: 0.8692 (t0) cc_final: 0.8447 (t0) REVERT: I 97 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: I 288 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: I 314 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6916 (p) REVERT: J 13 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: J 132 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8695 (t) REVERT: J 180 SER cc_start: 0.7915 (t) cc_final: 0.7626 (t) REVERT: J 281 MET cc_start: 0.8797 (mtp) cc_final: 0.8366 (mtm) REVERT: K 39 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8346 (mt-10) REVERT: K 97 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: K 217 ILE cc_start: 0.8336 (mt) cc_final: 0.8097 (mm) REVERT: K 292 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8731 (pp) REVERT: K 314 SER cc_start: 0.7244 (OUTLIER) cc_final: 0.6810 (p) REVERT: L 13 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: L 14 ASP cc_start: 0.8462 (t0) cc_final: 0.8047 (t70) REVERT: L 35 PHE cc_start: 0.8456 (m-80) cc_final: 0.8117 (m-80) REVERT: L 103 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.7709 (p) REVERT: L 153 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7790 (tttm) REVERT: L 180 SER cc_start: 0.7769 (t) cc_final: 0.7471 (t) REVERT: L 248 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8228 (mt) REVERT: L 267 GLU cc_start: 0.7688 (tp30) cc_final: 0.7241 (tp30) REVERT: L 278 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: L 288 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8362 (mp10) outliers start: 163 outliers final: 90 residues processed: 718 average time/residue: 1.4001 time to fit residues: 1177.3462 Evaluate side-chains 721 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 601 time to evaluate : 3.025 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 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 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 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 D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 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 E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 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 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain 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 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 103 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 176 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 339 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 332 optimal weight: 0.7980 chunk 304 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS C 97 GLN F 263 ASN H 12 HIS 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 = 0.3753 r_free = 0.3753 target = 0.155927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107166 restraints weight = 26288.682| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.66 r_work: 0.2956 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 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 = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29076 Z= 0.174 Angle : 0.530 6.402 39396 Z= 0.283 Chirality : 0.048 0.175 4668 Planarity : 0.003 0.030 4992 Dihedral : 7.171 58.989 4290 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.77 % Allowed : 16.03 % Favored : 79.20 % 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: 0.77 (0.14), residues: 3660 helix: 2.23 (0.14), residues: 1404 sheet: -0.66 (0.17), residues: 996 loop : -0.36 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 162 HIS 0.003 0.001 HIS C 123 PHE 0.021 0.002 PHE A 35 TYR 0.018 0.002 TYR E 146 ARG 0.005 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1296) hydrogen bonds : angle 4.46885 ( 3600) covalent geometry : bond 0.00403 (29076) covalent geometry : angle 0.52969 (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 750 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 600 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 103 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7678 (p) REVERT: A 132 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 248 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 260 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7866 (mtt180) REVERT: A 281 MET cc_start: 0.8827 (mtp) cc_final: 0.8406 (mtm) REVERT: A 288 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: B 14 ASP cc_start: 0.8269 (t0) cc_final: 0.7812 (t70) REVERT: B 52 ASP cc_start: 0.8671 (t0) cc_final: 0.8397 (t0) REVERT: B 62 GLU cc_start: 0.8199 (tp30) cc_final: 0.7940 (tp30) REVERT: B 97 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: B 267 GLU cc_start: 0.8235 (tp30) cc_final: 0.8009 (tp30) REVERT: B 288 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: B 314 SER cc_start: 0.7268 (OUTLIER) cc_final: 0.6992 (p) REVERT: C 115 MET cc_start: 0.9206 (mtp) cc_final: 0.8875 (mtp) REVERT: C 222 MET cc_start: 0.8599 (ptp) cc_final: 0.8345 (ptm) REVERT: C 260 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7726 (mtt180) REVERT: C 294 MET cc_start: 0.8942 (pmm) cc_final: 0.8688 (pmm) REVERT: C 314 SER cc_start: 0.7466 (OUTLIER) cc_final: 0.7030 (p) REVERT: D 37 ASN cc_start: 0.8481 (p0) cc_final: 0.8243 (p0) REVERT: D 78 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8275 (ttmt) REVERT: D 97 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: D 103 SER cc_start: 0.8515 (m) cc_final: 0.8132 (t) REVERT: D 217 ILE cc_start: 0.8279 (mt) cc_final: 0.7940 (mm) REVERT: D 245 TYR cc_start: 0.8518 (m-80) cc_final: 0.8253 (m-80) REVERT: D 261 ILE cc_start: 0.8382 (mt) cc_final: 0.8164 (mm) REVERT: D 267 GLU cc_start: 0.8258 (tp30) cc_final: 0.7762 (tp30) REVERT: D 292 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8550 (pp) REVERT: E 13 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: E 14 ASP cc_start: 0.8398 (t0) cc_final: 0.7976 (t70) REVERT: E 46 GLU cc_start: 0.8895 (pt0) cc_final: 0.8621 (pt0) REVERT: E 103 SER cc_start: 0.8426 (m) cc_final: 0.7926 (p) REVERT: E 153 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7824 (tttm) REVERT: E 180 SER cc_start: 0.7789 (t) cc_final: 0.7517 (t) REVERT: E 260 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7761 (mtm-85) REVERT: E 267 GLU cc_start: 0.7665 (tp30) cc_final: 0.7208 (tp30) REVERT: E 278 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: F 97 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: F 180 SER cc_start: 0.8195 (t) cc_final: 0.7938 (t) REVERT: F 288 GLN cc_start: 0.8508 (mt0) cc_final: 0.8180 (mt0) REVERT: F 292 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8745 (pp) REVERT: F 294 MET cc_start: 0.8715 (pmm) cc_final: 0.8355 (pmm) REVERT: F 314 SER cc_start: 0.7211 (OUTLIER) cc_final: 0.6786 (p) REVERT: G 78 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8284 (ttmt) REVERT: G 97 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: G 245 TYR cc_start: 0.8524 (m-80) cc_final: 0.8236 (m-80) REVERT: G 261 ILE cc_start: 0.8370 (mt) cc_final: 0.8165 (mm) REVERT: G 267 GLU cc_start: 0.8310 (tp30) cc_final: 0.7801 (tp30) REVERT: G 292 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8539 (pp) REVERT: H 35 PHE cc_start: 0.8455 (m-80) cc_final: 0.8175 (m-80) REVERT: H 222 MET cc_start: 0.8601 (ptp) cc_final: 0.8360 (ptm) REVERT: H 260 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7594 (mtt90) REVERT: H 294 MET cc_start: 0.8940 (pmm) cc_final: 0.8694 (pmm) REVERT: I 14 ASP cc_start: 0.8212 (t0) cc_final: 0.7952 (t70) REVERT: I 52 ASP cc_start: 0.8677 (t0) cc_final: 0.8420 (t0) REVERT: I 97 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: I 314 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.6947 (p) REVERT: J 13 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: J 132 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8677 (t) REVERT: J 260 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7886 (mtt180) REVERT: J 281 MET cc_start: 0.8825 (mtp) cc_final: 0.8410 (mtm) REVERT: K 97 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: K 217 ILE cc_start: 0.8267 (mt) cc_final: 0.8024 (mm) REVERT: K 288 GLN cc_start: 0.8495 (mt0) cc_final: 0.8154 (mt0) REVERT: K 292 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8752 (pp) REVERT: K 314 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6807 (p) REVERT: L 13 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: L 14 ASP cc_start: 0.8425 (t0) cc_final: 0.8004 (t70) REVERT: L 153 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7781 (tttm) REVERT: L 180 SER cc_start: 0.7769 (t) cc_final: 0.7499 (t) REVERT: L 260 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7783 (mtm-85) REVERT: L 267 GLU cc_start: 0.7673 (tp30) cc_final: 0.7235 (tp30) REVERT: L 278 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: L 288 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8362 (mp10) outliers start: 150 outliers final: 93 residues processed: 702 average time/residue: 1.4607 time to fit residues: 1192.8877 Evaluate side-chains 717 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 594 time to evaluate : 3.004 ------------------------------------------------------------------------------- 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 62 GLU Chi-restraints excluded: chain A residue 103 SER 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 286 LYS Chi-restraints excluded: chain A residue 288 GLN 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 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 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 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 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 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 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 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 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 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain 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 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 103 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 176 LYS 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: 7.9990 chunk 259 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 343 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 97 GLN C 130 HIS F 263 ASN H 97 GLN J 97 GLN K 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109398 restraints weight = 26674.628| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.71 r_work: 0.2997 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29076 Z= 0.102 Angle : 0.467 6.960 39396 Z= 0.249 Chirality : 0.046 0.164 4668 Planarity : 0.003 0.033 4992 Dihedral : 6.729 59.538 4287 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.91 % Allowed : 17.24 % 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: 0.81 (0.14), residues: 3660 helix: 2.37 (0.14), residues: 1404 sheet: -0.68 (0.17), residues: 948 loop : -0.46 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 162 HIS 0.003 0.001 HIS E 304 PHE 0.011 0.001 PHE L 35 TYR 0.014 0.001 TYR L 146 ARG 0.008 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 1296) hydrogen bonds : angle 4.35189 ( 3600) covalent geometry : bond 0.00227 (29076) covalent geometry : angle 0.46653 (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 727 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 604 time to evaluate : 6.399 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8659 (t) REVERT: A 148 GLU cc_start: 0.8156 (tt0) cc_final: 0.7866 (tt0) REVERT: A 248 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 281 MET cc_start: 0.8811 (mtp) cc_final: 0.8428 (mtm) REVERT: B 14 ASP cc_start: 0.8196 (t0) cc_final: 0.7756 (t70) REVERT: B 52 ASP cc_start: 0.8677 (t0) cc_final: 0.8392 (t0) REVERT: B 62 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: B 79 ILE cc_start: 0.8901 (pt) cc_final: 0.8667 (mm) REVERT: B 288 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: B 314 SER cc_start: 0.7086 (OUTLIER) cc_final: 0.6819 (p) REVERT: C 222 MET cc_start: 0.8576 (ptp) cc_final: 0.8300 (ptm) REVERT: C 248 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8077 (mt) REVERT: C 260 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7673 (mtt180) REVERT: C 294 MET cc_start: 0.8952 (pmm) cc_final: 0.8664 (pmm) REVERT: D 68 MET cc_start: 0.8662 (tpp) cc_final: 0.8406 (tpt) REVERT: D 78 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8284 (ttmt) REVERT: D 96 ARG cc_start: 0.8671 (mtm180) cc_final: 0.8401 (mtt180) REVERT: D 97 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7123 (mp-120) REVERT: D 103 SER cc_start: 0.8437 (m) cc_final: 0.8090 (t) REVERT: D 217 ILE cc_start: 0.8249 (mt) cc_final: 0.7896 (mm) REVERT: D 245 TYR cc_start: 0.8482 (m-80) cc_final: 0.8237 (m-80) REVERT: D 261 ILE cc_start: 0.8332 (mt) cc_final: 0.8126 (mm) REVERT: D 267 GLU cc_start: 0.8245 (tp30) cc_final: 0.7763 (tp30) REVERT: D 292 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8549 (pp) REVERT: E 14 ASP cc_start: 0.8384 (t0) cc_final: 0.7967 (t70) REVERT: E 46 GLU cc_start: 0.8919 (pt0) cc_final: 0.8674 (pt0) REVERT: E 153 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7797 (tttm) REVERT: E 180 SER cc_start: 0.7775 (t) cc_final: 0.7518 (t) REVERT: E 260 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7796 (mtm-85) REVERT: E 267 GLU cc_start: 0.7707 (tp30) cc_final: 0.7200 (tp30) REVERT: E 278 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: F 180 SER cc_start: 0.8175 (t) cc_final: 0.7910 (t) REVERT: F 278 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: F 288 GLN cc_start: 0.8462 (mt0) cc_final: 0.8091 (mt0) REVERT: F 292 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8768 (pp) REVERT: F 294 MET cc_start: 0.8741 (pmm) cc_final: 0.8376 (pmm) REVERT: F 314 SER cc_start: 0.7023 (OUTLIER) cc_final: 0.6650 (p) REVERT: G 68 MET cc_start: 0.8677 (tpp) cc_final: 0.8451 (tpt) REVERT: G 78 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: G 245 TYR cc_start: 0.8502 (m-80) cc_final: 0.8280 (m-80) REVERT: G 267 GLU cc_start: 0.8295 (tp30) cc_final: 0.7791 (tp30) REVERT: G 292 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8539 (pp) REVERT: H 35 PHE cc_start: 0.8450 (m-80) cc_final: 0.8196 (m-80) REVERT: H 248 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8064 (mt) REVERT: H 260 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7632 (mtt180) REVERT: H 294 MET cc_start: 0.8913 (pmm) cc_final: 0.8590 (pmm) REVERT: H 314 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6770 (p) REVERT: I 14 ASP cc_start: 0.8106 (t0) cc_final: 0.7841 (t70) REVERT: I 52 ASP cc_start: 0.8689 (t0) cc_final: 0.8425 (t0) REVERT: I 79 ILE cc_start: 0.8899 (pt) cc_final: 0.8661 (mm) REVERT: I 267 GLU cc_start: 0.8084 (tp30) cc_final: 0.7881 (tp30) REVERT: I 288 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: J 132 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8655 (t) REVERT: J 281 MET cc_start: 0.8786 (mtp) cc_final: 0.8389 (mtm) REVERT: K 180 SER cc_start: 0.8136 (t) cc_final: 0.7873 (t) REVERT: K 217 ILE cc_start: 0.8241 (mt) cc_final: 0.7977 (mm) REVERT: K 247 ILE cc_start: 0.9013 (mt) cc_final: 0.8794 (mm) REVERT: K 288 GLN cc_start: 0.8443 (mt0) cc_final: 0.8110 (mt0) REVERT: K 292 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8771 (pp) REVERT: L 13 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: L 14 ASP cc_start: 0.8412 (t0) cc_final: 0.7989 (t70) REVERT: L 153 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7778 (tttm) REVERT: L 180 SER cc_start: 0.7767 (t) cc_final: 0.7517 (t) REVERT: L 248 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8160 (mt) REVERT: L 260 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7567 (mtm-85) REVERT: L 267 GLU cc_start: 0.7668 (tp30) cc_final: 0.7191 (tp30) REVERT: L 278 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: L 288 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8363 (mp10) outliers start: 123 outliers final: 77 residues processed: 693 average time/residue: 1.5222 time to fit residues: 1240.8263 Evaluate side-chains 699 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 598 time to evaluate : 2.966 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 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 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 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 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 314 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 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 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 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 176 LYS 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: 6.9990 chunk 274 optimal weight: 0.4980 chunk 224 optimal weight: 0.0970 chunk 297 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 318 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 97 GLN F 263 ASN H 130 HIS J 97 GLN K 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111621 restraints weight = 26571.926| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.72 r_work: 0.3023 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29076 Z= 0.096 Angle : 0.458 7.240 39396 Z= 0.243 Chirality : 0.046 0.164 4668 Planarity : 0.003 0.035 4992 Dihedral : 6.535 59.977 4287 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.53 % Allowed : 17.56 % Favored : 78.91 % 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: 2.49 (0.14), residues: 1404 sheet: -0.72 (0.16), residues: 984 loop : -0.36 (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 H 193 PHE 0.012 0.001 PHE E 35 TYR 0.012 0.001 TYR L 146 ARG 0.007 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 1296) hydrogen bonds : angle 4.25209 ( 3600) covalent geometry : bond 0.00213 (29076) covalent geometry : angle 0.45769 (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 741 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 630 time to evaluate : 3.217 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8688 (t) REVERT: A 248 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 260 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7690 (mtm-85) REVERT: A 281 MET cc_start: 0.8809 (mtp) cc_final: 0.8432 (mtm) REVERT: B 14 ASP cc_start: 0.8135 (t0) cc_final: 0.7685 (t70) REVERT: B 38 GLN cc_start: 0.8261 (mm110) cc_final: 0.7993 (mm110) REVERT: B 52 ASP cc_start: 0.8652 (t0) cc_final: 0.8388 (t0) REVERT: B 79 ILE cc_start: 0.8945 (pt) cc_final: 0.8705 (mm) REVERT: B 267 GLU cc_start: 0.8080 (tp30) cc_final: 0.7868 (tp30) REVERT: B 288 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: B 314 SER cc_start: 0.7056 (OUTLIER) cc_final: 0.6806 (p) REVERT: C 222 MET cc_start: 0.8547 (ptp) cc_final: 0.8269 (ptm) REVERT: C 248 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8121 (mt) REVERT: C 260 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7623 (mtt180) REVERT: C 294 MET cc_start: 0.8910 (pmm) cc_final: 0.8585 (pmm) REVERT: C 298 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8771 (mm-30) REVERT: D 22 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.8170 (mtt90) REVERT: D 78 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: D 97 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7156 (mp-120) REVERT: D 103 SER cc_start: 0.8403 (m) cc_final: 0.8080 (t) REVERT: D 217 ILE cc_start: 0.8252 (mt) cc_final: 0.7924 (mm) REVERT: D 267 GLU cc_start: 0.8249 (tp30) cc_final: 0.7845 (tp30) REVERT: D 292 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 14 ASP cc_start: 0.8374 (t0) cc_final: 0.7953 (t70) REVERT: E 33 LYS cc_start: 0.8450 (pttt) cc_final: 0.8242 (pttp) REVERT: E 46 GLU cc_start: 0.8852 (pt0) cc_final: 0.8604 (pt0) REVERT: E 180 SER cc_start: 0.7704 (t) cc_final: 0.7461 (t) REVERT: E 248 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8181 (mt) REVERT: E 260 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7534 (mtm-85) REVERT: E 267 GLU cc_start: 0.7707 (tp30) cc_final: 0.7208 (tp30) REVERT: E 278 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: E 288 GLN cc_start: 0.8709 (mt0) cc_final: 0.8257 (mp10) REVERT: F 180 SER cc_start: 0.8257 (t) cc_final: 0.8008 (t) REVERT: F 278 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: F 288 GLN cc_start: 0.8445 (mt0) cc_final: 0.8081 (mt0) REVERT: F 294 MET cc_start: 0.8749 (pmm) cc_final: 0.8262 (pmm) REVERT: G 21 ASP cc_start: 0.8326 (m-30) cc_final: 0.8076 (m-30) REVERT: G 78 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8286 (ttmt) REVERT: G 97 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: G 103 SER cc_start: 0.8413 (m) cc_final: 0.8087 (t) REVERT: G 267 GLU cc_start: 0.8272 (tp30) cc_final: 0.7793 (tp30) REVERT: G 292 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8525 (pp) REVERT: H 35 PHE cc_start: 0.8452 (m-80) cc_final: 0.8174 (m-80) REVERT: H 248 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8093 (mt) REVERT: H 260 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7632 (mtt180) REVERT: H 294 MET cc_start: 0.8926 (pmm) cc_final: 0.8621 (pmm) REVERT: H 314 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6717 (p) REVERT: I 14 ASP cc_start: 0.8068 (t0) cc_final: 0.7813 (t70) REVERT: I 21 ASP cc_start: 0.8379 (m-30) cc_final: 0.7827 (m-30) REVERT: I 38 GLN cc_start: 0.8284 (mm110) cc_final: 0.8015 (mm110) REVERT: I 52 ASP cc_start: 0.8658 (t0) cc_final: 0.8381 (t0) REVERT: I 79 ILE cc_start: 0.8957 (pt) cc_final: 0.8717 (mm) REVERT: I 220 ASP cc_start: 0.8634 (t0) cc_final: 0.8422 (t0) REVERT: I 314 SER cc_start: 0.7000 (OUTLIER) cc_final: 0.6728 (p) REVERT: J 96 ARG cc_start: 0.8830 (mtm180) cc_final: 0.8582 (mtm180) REVERT: J 132 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8648 (t) REVERT: J 222 MET cc_start: 0.8580 (ptp) cc_final: 0.8347 (ptp) REVERT: J 248 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8101 (mt) REVERT: J 260 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7701 (mtm-85) REVERT: J 281 MET cc_start: 0.8815 (mtp) cc_final: 0.8453 (mtm) REVERT: K 127 MET cc_start: 0.9156 (ttm) cc_final: 0.8833 (tpp) REVERT: K 180 SER cc_start: 0.8217 (t) cc_final: 0.7944 (t) REVERT: K 217 ILE cc_start: 0.8242 (mt) cc_final: 0.7960 (mm) REVERT: K 247 ILE cc_start: 0.8964 (mt) cc_final: 0.8755 (mm) REVERT: K 278 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: K 282 LYS cc_start: 0.7800 (tttt) cc_final: 0.7187 (ttpp) REVERT: K 292 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8778 (pp) REVERT: K 314 SER cc_start: 0.7021 (OUTLIER) cc_final: 0.6616 (p) REVERT: L 14 ASP cc_start: 0.8391 (t0) cc_final: 0.7977 (t70) REVERT: L 39 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8092 (tt0) REVERT: L 153 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7681 (tttm) REVERT: L 180 SER cc_start: 0.7695 (t) cc_final: 0.7448 (t) REVERT: L 222 MET cc_start: 0.8573 (ptp) cc_final: 0.8260 (ptp) REVERT: L 248 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8197 (mt) REVERT: L 260 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7575 (mtm-85) REVERT: L 267 GLU cc_start: 0.7658 (tp30) cc_final: 0.7176 (tp30) REVERT: L 278 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: L 288 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8383 (mp10) outliers start: 111 outliers final: 64 residues processed: 716 average time/residue: 1.4637 time to fit residues: 1215.6348 Evaluate side-chains 705 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 616 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 278 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 314 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 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU 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 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 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 278 GLU 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 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 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 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 132 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL 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 62 GLU Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 278 GLU 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 K residue 314 SER Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU 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: 0.0000 chunk 136 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 140 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 252 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 J 288 GLN K 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112195 restraints weight = 26637.585| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.53 r_work: 0.3033 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 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 = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29076 Z= 0.090 Angle : 0.452 7.618 39396 Z= 0.239 Chirality : 0.046 0.161 4668 Planarity : 0.003 0.042 4992 Dihedral : 5.834 59.801 4275 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.96 % Allowed : 18.07 % 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: 0.93 (0.14), residues: 3660 helix: 2.55 (0.14), residues: 1404 sheet: -0.74 (0.16), residues: 984 loop : -0.36 (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 F 250 PHE 0.012 0.001 PHE E 35 TYR 0.013 0.001 TYR I 245 ARG 0.009 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 1296) hydrogen bonds : angle 4.19943 ( 3600) covalent geometry : bond 0.00198 (29076) covalent geometry : angle 0.45216 (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 712 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 619 time to evaluate : 3.139 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8641 (t) REVERT: A 260 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7692 (mtm-85) REVERT: A 281 MET cc_start: 0.8789 (mtp) cc_final: 0.8443 (mtm) REVERT: B 14 ASP cc_start: 0.8096 (t0) cc_final: 0.7652 (t70) REVERT: B 21 ASP cc_start: 0.8342 (m-30) cc_final: 0.7954 (m-30) REVERT: B 38 GLN cc_start: 0.8179 (mm110) cc_final: 0.7942 (mm110) REVERT: B 52 ASP cc_start: 0.8652 (t0) cc_final: 0.8376 (t0) REVERT: B 288 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: B 314 SER cc_start: 0.6934 (OUTLIER) cc_final: 0.6687 (p) REVERT: C 22 ARG cc_start: 0.8881 (mtt90) cc_final: 0.8608 (mtt90) REVERT: C 181 ILE cc_start: 0.7606 (mt) cc_final: 0.7309 (mm) REVERT: C 205 MET cc_start: 0.6426 (ttt) cc_final: 0.6148 (mtp) REVERT: C 222 MET cc_start: 0.8588 (ptp) cc_final: 0.8348 (ptm) REVERT: C 260 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7641 (mtt180) REVERT: C 294 MET cc_start: 0.8882 (pmm) cc_final: 0.8534 (pmm) REVERT: C 298 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8742 (mm-30) REVERT: D 97 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7122 (mp-120) REVERT: D 103 SER cc_start: 0.8401 (m) cc_final: 0.8090 (t) REVERT: D 217 ILE cc_start: 0.8274 (mt) cc_final: 0.7917 (mm) REVERT: D 267 GLU cc_start: 0.8178 (tp30) cc_final: 0.7807 (tp30) REVERT: E 14 ASP cc_start: 0.8347 (t0) cc_final: 0.7931 (t70) REVERT: E 46 GLU cc_start: 0.8801 (pt0) cc_final: 0.8551 (pt0) REVERT: E 180 SER cc_start: 0.7652 (t) cc_final: 0.7412 (t) REVERT: E 260 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7548 (mtm-85) REVERT: E 267 GLU cc_start: 0.7674 (tp30) cc_final: 0.7195 (tp30) REVERT: E 288 GLN cc_start: 0.8707 (mt0) cc_final: 0.8248 (mp10) REVERT: F 79 ILE cc_start: 0.8868 (pt) cc_final: 0.8650 (mm) REVERT: F 180 SER cc_start: 0.8301 (t) cc_final: 0.8009 (t) REVERT: F 217 ILE cc_start: 0.8173 (mt) cc_final: 0.7888 (mm) REVERT: F 278 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: F 288 GLN cc_start: 0.8422 (mt0) cc_final: 0.8080 (mt0) REVERT: F 294 MET cc_start: 0.8743 (pmm) cc_final: 0.8364 (pmm) REVERT: G 21 ASP cc_start: 0.8256 (m-30) cc_final: 0.7996 (m-30) REVERT: G 38 GLN cc_start: 0.7949 (mm110) cc_final: 0.7723 (mm-40) REVERT: G 78 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8310 (ttmt) REVERT: G 103 SER cc_start: 0.8410 (m) cc_final: 0.8090 (t) REVERT: G 217 ILE cc_start: 0.8230 (mt) cc_final: 0.7865 (mm) REVERT: G 267 GLU cc_start: 0.8234 (tp30) cc_final: 0.7785 (tp30) REVERT: H 35 PHE cc_start: 0.8457 (m-80) cc_final: 0.8228 (m-80) REVERT: H 222 MET cc_start: 0.8611 (ptp) cc_final: 0.8365 (ptm) REVERT: H 260 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7635 (mtt180) REVERT: H 294 MET cc_start: 0.8924 (pmm) cc_final: 0.8645 (pmm) REVERT: H 314 SER cc_start: 0.7207 (OUTLIER) cc_final: 0.6766 (p) REVERT: I 14 ASP cc_start: 0.8046 (t0) cc_final: 0.7832 (t70) REVERT: I 21 ASP cc_start: 0.8358 (m-30) cc_final: 0.8003 (m-30) REVERT: I 38 GLN cc_start: 0.8167 (mm110) cc_final: 0.7924 (mm110) REVERT: I 52 ASP cc_start: 0.8651 (t0) cc_final: 0.8369 (t0) REVERT: I 220 ASP cc_start: 0.8604 (t0) cc_final: 0.8363 (t0) REVERT: I 281 MET cc_start: 0.8642 (mtm) cc_final: 0.8332 (mtm) REVERT: I 288 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: I 314 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6706 (p) REVERT: J 132 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8612 (t) REVERT: J 260 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7683 (mtm-85) REVERT: J 281 MET cc_start: 0.8767 (mtp) cc_final: 0.8431 (mtm) REVERT: K 79 ILE cc_start: 0.8871 (pt) cc_final: 0.8645 (mm) REVERT: K 127 MET cc_start: 0.9132 (ttm) cc_final: 0.8816 (tpp) REVERT: K 180 SER cc_start: 0.8234 (t) cc_final: 0.7989 (t) REVERT: K 217 ILE cc_start: 0.8235 (mt) cc_final: 0.7951 (mm) REVERT: K 278 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: K 282 LYS cc_start: 0.7836 (tttt) cc_final: 0.7223 (ttpp) REVERT: K 288 GLN cc_start: 0.8427 (mt0) cc_final: 0.8098 (mt0) REVERT: K 292 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8741 (pp) REVERT: K 314 SER cc_start: 0.6986 (OUTLIER) cc_final: 0.6586 (p) REVERT: L 14 ASP cc_start: 0.8390 (t0) cc_final: 0.7991 (t70) REVERT: L 180 SER cc_start: 0.7673 (t) cc_final: 0.7436 (t) REVERT: L 222 MET cc_start: 0.8591 (ptp) cc_final: 0.8343 (ptp) REVERT: L 260 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7576 (mtm-85) REVERT: L 267 GLU cc_start: 0.7659 (tp30) cc_final: 0.7195 (tp30) REVERT: L 288 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8368 (mp10) outliers start: 93 outliers final: 61 residues processed: 690 average time/residue: 1.5813 time to fit residues: 1274.6340 Evaluate side-chains 673 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 598 time to evaluate : 3.217 ------------------------------------------------------------------------------- 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 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 B residue 314 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 278 GLU Chi-restraints excluded: chain C residue 292 ILE 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 237 LEU Chi-restraints excluded: chain D residue 249 THR 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 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 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 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 169 SER Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL 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 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 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 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 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 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 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 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: 8.9990 chunk 355 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 294 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 97 GLN F 263 ASN J 97 GLN J 288 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108852 restraints weight = 26634.783| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.59 r_work: 0.2977 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 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 = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29076 Z= 0.125 Angle : 0.489 7.514 39396 Z= 0.258 Chirality : 0.046 0.169 4668 Planarity : 0.003 0.042 4992 Dihedral : 5.859 57.607 4273 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.99 % Allowed : 18.45 % Favored : 78.56 % 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: 2.49 (0.14), residues: 1404 sheet: -0.77 (0.17), residues: 948 loop : -0.42 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS J 123 PHE 0.015 0.001 PHE C 35 TYR 0.014 0.002 TYR I 245 ARG 0.009 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1296) hydrogen bonds : angle 4.24079 ( 3600) covalent geometry : bond 0.00287 (29076) covalent geometry : angle 0.48878 (39396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33648.79 seconds wall clock time: 583 minutes 13.83 seconds (34993.83 seconds total)